Compositions and methods for contolling plant pests

ABSTRACT

Novel insecticidal proteins isolated from  Bacillus thuringiensis  that are active against lepidopteran insect pests are disclosed. The DNA encoding the insecticidal proteins can be used to transform various prokaryotic and eukaryotic organisms to express the insecticidal proteins. These recombinant organisms can be used to control lepidopteran insects in various environments.

This is a divisional application of pending U.S. application Ser. No.15/534,199, filed Jun. 8, 2017, which is a 371 of International PatentApplication No. PCT/US15/63620, filed Dec. 3, 2015 and published asWO2016/094165 on Jun. 6, 2016, which claims priority to U.S. ProvisionalPatent Application No. 62/090900, filed Dec. 12, 2014, all of which areincorporated by reference herein in their entirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The official copy of the sequence listing is submitted electronicallyvia EFS-Web as an ASCII formatted sequence listing with a file named“80670-US-L-ORG-NAT-1_SeqList.txt”, created on Dec. 5, 2014, and havinga size of 170 kilobytes and is filed concurrently with thespecification. The sequence listing contained in this ASCII formatteddocument is part of the specification and is herein incorporated byreference in its entirety.

FIELD OF THE INVENTION

This invention relates to pesticidal proteins and the nucleic acidmolecules that encode them, as well as compositions and methods forcontrolling plant pests.

BACKGROUND

Bacillus thuringiensis (Bt) is a gram-positive spore forming soilbacterium characterized by its ability to produce crystalline inclusionsthat are specifically toxic to certain orders and species of plantpests, including insects, but are harmless to plants and othernon-target organisms. For this reason, compositions comprising Bacillusthuringiensis strains or their insecticidal proteins can be used asenvironmentally-acceptable insecticides to control agricultural insectpests or insect vectors of a variety of human or animal diseases.

Crystal (Cry) proteins from Bacillus thuringiensis have potentinsecticidal activity against predominantly lepidopteran, dipteran, andcoleopteran larvae. These proteins also have shown activity againstpests in the Orders Hymenoptera, Homoptera, Phthiraptera, Mallophaga,and Acari pest orders, as well as other invertebrate orders such asNemathelminthes, Platyhelminthes, and Sarcomastigorphora (Feitelson, J.1993. The Bacillus Thuringiensis family tree. In Advanced EngineeredPesticides. Marcel Dekker, Inc., New York, N.Y.). These proteins wereoriginally classified as CryI to CryVI based primarily on theirinsecticidal activity. The major classes were Lepidoptera-specific (I),Lepidoptera- and Diptera-specific (II), Coleoptera-specific (III),Diptera-specific (IV), and nematode-specific (V) and (VI). The proteinswere further classified into subfamilies; more highly related proteinswithin each family were assigned divisional letters such as CryIA,CryIB, CryIC, etc. Even more closely related proteins within eachdivision were given names such as CryIC(a), CryIC(b), etc. The terms“Cry toxin” and “delta-endotoxin” have been used interchangeably withthe term “Cry protein.” Current nomenclature for Cry proteins and genesis based upon amino acid sequence homology rather than insect targetspecificity (Crickmore et al. (1998) Microbiol. Mol. Biol. Rev.62:807-813). In this more accepted classification, each toxin isassigned a unique name incorporating a primary rank (an Arabic number),a secondary rank (an uppercase letter), a tertiary rank (a lowercaseletter), and a quaternary rank (another Arabic number). In the currentclassification, Roman numerals have been exchanged for Arabic numeralsin the primary rank. For example, “CryIA(a)” under the oldernomenclature is now “Cry1Aa” under the current nomenclature.

Cry proteins are globular protein molecules which accumulate asprotoxins in crystalline form during the sporulation stage of Bt. Afteringestion by a pest, the crystals are typically solubilized to releaseprotoxins, which can range in size, for example, from 130-140 kDa forlepidopteran-active Cry proteins and 60-80 kDa for coleopteran-activeCry proteins. Protoxins are converted into mature toxic fragments(approximately 60-70 kDa N terminal region) by gut proteases in thetarget pest. Many of these proteins are quite toxic to specific targetinsects, but harmless to plants and other non-targeted organisms.

Cry proteins generally have five conserved sequence domains, and threeconserved structural domains (see, for example, de Maagd et al. (2001)Trends Genetics 17:193-199). The first conserved structural domain,called Domain I, typically consists of seven alpha helices and isinvolved in membrane insertion and pore formation. Domain II typicallyconsists of three beta-sheets arranged in a Greek key configuration, anddomain III typically consists of two antiparallel beta-sheets in‘jelly-roll’ formation (de Maagd et al., 2001, supra). Domains II andIII are involved in receptor recognition and binding, and are thereforeconsidered determinants of toxin specificity.

Numerous commercially valuable plants, including common agriculturalcrops, are susceptible to attack by plant pests including insect andnematode pests, causing substantial reductions in crop yield andquality. For example, plant pests are a major factor in the loss of theworld's important agricultural crops. About $8 billion are lost everyyear in the United States alone due to infestations of non-mammalianpests including insects. In addition to losses in field crops, insectpests are also a burden to vegetable and fruit growers, to producers ofornamental flowers, and to home gardeners.

Insect pests are mainly controlled by intensive applications of chemicalpesticides, which are active through inhibition of insect growth,prevention of insect feeding or reproduction, or cause death. Biologicalpest control agents, such as Bacillus thuringiensis strains expressingpesticidal toxins such as Cry proteins, have also been applied to cropplants with satisfactory results, offering an alternative or complimentto chemical pesticides. The genes coding for some of these Cry proteinshave been isolated and their expression in heterologous hosts such astransgenic plants have been shown to provide another tool for thecontrol of economically important insect pests.

Good insect control can thus be reached, but certain chemicals cansometimes also affect non-target beneficial insects and certainbiologicals have a very narrow spectrum of activity. In addition, thecontinued use of certain chemical and biological control methodsheightens the chance for insect pests to develop resistance to suchcontrol measures. This has been partially alleviated by variousresistance management practices, but there remains a need to discovernew and effective pest control agents that provide an economic benefitto farmers and that are environmentally acceptable. Particularly neededare control agents that are targeted to a wider spectrum of economicallyimportant insect pests and that efficiently control insect strains thatare or could become resistant to existing insect control agents.

SUMMARY

In view of these needs, it is an object of the present invention toprovide new pest control agents by providing novel genes and pesticidalproteins that may be used to control a variety of plant pests.

The invention provides compositions and methods for conferringpesticidal activity to bacteria, plants, plant cells, tissues and seeds.In particular, chimeric genes comprising novel polynucleotides thatencode Cry proteins isolated from Bacillus thuringiensis (Bt) andsequences substantially identical thereto, whose expression results inproteins with toxicity to economically important insect pests,particularly insect pests that infest plants, are provided. Theinvention is further drawn to the novel Cry proteins resulting from theexpression of the nucleic acid sequences, and to compositions andformulations containing the Cry proteins, which are toxic to insects byinhibiting the ability of insect pests to survive, grow and reproduce,or of limiting insect-related damage or loss to crop plants. Cryproteins of the invention include native Cry proteins and mutant Cryproteins that have one or more amino acid substitutions, additions ordeletions. Examples of mutant Cry proteins includes without limitationthose that are mutated to have a broader spectrum of activity than theirnative Cry protein counterparts or those mutated to introduce an epitopeto generate antibodies that differentially recognize the mutated proteinfrom the native protein. The novel Cry proteins of the invention arehighly active against insect pests. For example, the Cry proteins of theinvention can be used to control one or more economically importantinsects pests such as black cutworm (Agrotis ipsilon), European cornborer (Ostrinia nubilalis), fall armyworm (Spodoptera frugiperda), cornearworm (Helicoverpa zea), sugarcane borer (Diatraea saccharalis),velvetbean caterpillar (Anticarsia gemmatalis), soybean looper(Chrysodeixis includes), southwest corn borer (Diatraea grandiosella),western bean cutworm (Richia albicosta), tobacco budworm (Heliothisvirescens), Asian corn borer (Ostrinia furnacalis), cotton bollworm(Helicoverpa armigera), striped stem borer (Chilo suppressalis), pinkstem borer (Sesamia calamistis), rice leaffolder (Cnaphalocrocismedinalis), and the like.

The invention also provides synthetic polynucleotides that encode theCry proteins of the invention and have one or more codons optimized forexpression in transgenic organisms such as bacteria and plants.

The invention is further drawn to expression cassettes and recombinantvectors comprising a polynucleotide that encodes a Cry protein of theinvention. The invention also provides transformed bacteria, plants,plant cells, tissues, and seeds comprising a chimeric gene, or anexpression cassette or a recombinant vector which comprise apolynucleotide encoding a Cry protein of the invention.

The invention is also drawn to methods of using the polynucleotides, forexample in DNA constructs or chimeric genes or expression cassettes orrecombinant vectors for transformation and expression in organisms,including microorganisms and plants. The nucleotide or amino acidsequences may be synthetic sequences that have been designed forexpression in an organism including, but not limited to, a microorganismor a plant or in making hybrid toxins with enhanced pesticidal activity.The invention is further drawn to methods of making the Cry proteins andto methods of using the nucleic acid sequences, for example inmicroorganisms to control insects or in transgenic plants to conferprotection from insect damage, and to methods of using the Cry proteins,and compositions and formulations comprising the Cry proteins, forexample applying the Cry proteins or compositions or formulations toinsect-infested areas, or to prophylactically treat insect-susceptibleareas or plants to confer protection against the insect pests. Thenucleotide or amino acid sequences may be synthetic sequences that havebeen designed for expression in an organism including, but not limitedto, a microorganism or a plant.

The compositions and methods of the invention are useful for theproduction of organisms that are toxic to insects, specifically bacteriaand plants. These organisms and compositions derived from them aredesirable for agricultural purposes. The compositions of the inventionare also useful for generating altered or improved Cry proteins thathave pesticidal activity, or for detecting the presence of Cry proteinor nucleic acids in products or organisms.

These and other features, aspects, and advantages of the invention willbecome better understood with reference to the following detaileddescription and claims.

BRIEF DESCRIPTION OF THE SEQUENCES IN THE SEQUENCE LISTING

SEQ ID NO: 1 represents a nucleotide sequence encoding a BT-0009protein.

SEQ ID NO: 2 represents a nucleotide sequence encoding a BT-0012protein.

SEQ ID NO: 3 represents a nucleotide sequence encoding a BT-0013protein.

SEQ ID NO: 4 represents a nucleotide sequence encoding a BT-0023protein.

SEQ ID NO: 5 represents a nucleotide sequence encoding a BT-0067protein.

SEQ ID NO:6 represents a codon optimized sequence encoding a BT-0009protein.

SEQ ID NO: 7 represents a codon optimized sequence encoding a BT-0012protein.

SEQ ID NO:8 represents a codon optimized sequence encoding a BT-0013protein.

SEQ ID NO:9 represents a codon optimized sequence encoding a BT-0023protein.

SEQ ID NO:10 represents a codon optimized sequence encoding a BT-0067protein.

SEQ ID NO:11 represents a nucleotide sequence encoding a mutant BT-0009protein.

SEQ ID NO:12 represents a nucleotide sequence encoding a mutant BT-0012protein.

SEQ ID NO:13 represents a nucleotide sequence encoding a mutant BT-0013protein.

SEQ ID NO:14 represents a nucleotide sequence encoding a mutant BT-0023protein.

SEQ ID NO:15 represents a nucleotide sequence encoding a mutant BT-0067protein

SEQ ID NO:16 represents an amino acid sequence of a BT-0009 protein.

SEQ ID NO:17 represents an amino acid sequence of a BT-0012 protein.

SEQ ID NO:18 represents an amino acid sequence of a BT-0013 protein.

SEQ ID NO:19 represents an amino acid sequence of a BT-0023 protein.

SEQ ID NO:20 represents an amino acid sequence of a BT-0067 protein.

SEQ ID NO:21 represents an amino acid sequence of a mutant BT-0009protein.

SEQ ID NO:22 represents an amino acid sequence of a mutant BT-0012protein.

SEQ ID NO:23 represents an amino acid sequence of a mutant BT-0013protein.

SEQ ID NO:24 represents an amino acid sequence of a mutant BT-0023protein

SEQ ID NO:25 represents an amino acid sequence of a mutant BT-0067protein.

SEQ ID NOS:26-31 represent primers useful in the invention.

DETAILED DESCRIPTION

This description is not intended to be a detailed catalog of all thedifferent ways in which the invention may be implemented, or all thefeatures that may be added to the instant invention. For example,features illustrated with respect to one embodiment may be incorporatedinto other embodiments, and features illustrated with respect to aparticular embodiment may be deleted from that embodiment. Thus, theinvention contemplates that in some embodiments of the invention, anyfeature or combination of features set forth herein can be excluded oromitted. In addition, numerous variations and additions to the variousembodiments suggested herein will be apparent to those skilled in theart in light of the instant disclosure, which do not depart from theinstant invention. Hence, the following descriptions are intended toillustrate some particular embodiments of the invention, and not toexhaustively specify all permutations, combinations and variationsthereof.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The terminology used in thedescription of the invention herein is for the purpose of describingparticular embodiments only and is not intended to be limiting of theinvention. It is also to be understood that the terminology used hereinis for the purpose of describing particular embodiments only, and is notintended to limit the scope of the present invention.

Definitions

As used herein and in the appended claims, the singular forms “a,”“and,” and “the” include plural reference unless the context clearlydictates otherwise. Thus, for example, reference to “a plant” is areference to one or more plants and includes equivalents thereof knownto those skilled in the art, and so forth. As used herein, the word “or”means any one member of a particular list and also includes anycombination of members of that list (i.e., includes also “and”).

The term “about” is used herein to mean approximately, roughly, around,or in the region of. When the term “about” is used in conjunction with anumerical range, it modifies that range by extending the boundariesabove and below the numerical values set forth. In general, the term“about” is used herein to modify a numerical value above and below thestated value by a variance of 20 percent, preferably 10 percent up ordown (higher or lower). With regard to a temperature the term “about”means±1° C., preferably ±0.5° C. Where the term “about” is used in thecontext of this invention (e.g., in combinations with temperature ormolecular weight values) the exact value (i.e., without “about”) ispreferred.

By “activity” of a toxic Cry protein of the invention is meant that thetoxic protein functions as an orally active insect control agent, has atoxic effect, or is able to disrupt or deter insect feeding, which mayor may not cause death of the insect. When a toxic protein of theinvention is delivered to the insect, the result is typically death ofthe insect, or the insect does not feed upon the source that makes thetoxic protein available to the insect.

As used herein, the term “amplified” means the construction of multiplecopies of a nucleic acid molecule or multiple copies complementary tothe nucleic acid molecule using at least one of the nucleic acidmolecules as a template. Amplification systems include the polymerasechain reaction (PCR) system, ligase chain reaction (LCR) system, nucleicacid sequence based amplification (NASBA, Cangene, Mississauga,Ontario), Q-Beta Replicase systems, transcription-based amplificationsystem (TAS), and strand displacement amplification (SDA). See, e.g.,Diagnostic Molecular Microbiology: Principles and Applications, PERSINGet al., Ed., American Society for Microbiology, Washington, D.C. (1993).The product of amplification is termed an “amplicon.”

The term “chimeric construct” or “chimeric gene” or “chimericpolynucleotide” or “chimeric nucleic acid” (or similar terms) as usedherein refers to a construct or molecule comprising two or morepolynucleotides of different origin assembled into a single nucleic acidmolecule. The term “chimeric construct”, “chimeric gene”, “chimericpolynucleotide” or “chimeric nucleic acid” refers to any construct ormolecule that contains, without limitation, (1) polynucleotides (e.g.,DNA), including regulatory and coding polynucleotides that are not foundtogether in nature (i.e., at least one of the polynucleotides in theconstruct is heterologous with respect to at least one of its otherpolynucleotides), or (2) polynucleotides encoding parts of proteins notnaturally adjoined, or (3) parts of promoters that are not naturallyadjoined. Further, a chimeric construct, chimeric gene, chimericpolynucleotide or chimeric nucleic acid may comprise regulatorypolynucleotides and coding polynucleotides that are derived fromdifferent sources, or comprise regulatory polynucleotides and codingpolynucleotides derived from the same source, but arranged in a mannerdifferent from that found in nature. In some embodiments of theinvention, the chimeric construct, chimeric gene, chimericpolynucleotide or chimeric nucleic acid comprises an expression cassettecomprising a polynucleotide of the invention under the control ofregulatory polynucleotides, particularly under the control of regulatorypolynucleotides functional in plants or bacteria.

A “coding sequence” is a nucleic acid sequence that is transcribed intoRNA such as mRNA, rRNA, tRNA, snRNA, sense RNA or antisense RNA.Preferably the RNA is then translated in an organism to produce aprotein.

As used herein, a “codon optimized” sequence means a nucleotide sequenceof a recombinant, transgenic, or synthetic polynucleotide wherein thecodons are chosen to reflect the particular codon bias that a host cellor organism may have. This is typically done in such a way so as topreserve the amino acid sequence of the polypeptide encoded by the codonoptimized nucleotide sequence. In certain embodiments, the DNA sequenceof the recombinant DNA construct includes sequence that has been codonoptimized for the cell (e.g., an animal, plant, or fungal cell) in whichthe construct is to be expressed. For example, a construct to beexpressed in a plant cell can have all or parts of its sequence (e.g.,the first gene suppression element or the gene expression element) codonoptimized for expression in a plant. See, for example, U.S. Pat. No.6,121,014, incorporated herein by reference.

To “control” insects means to inhibit, through a toxic effect, theability of insect pests to survive, grow, feed, and/or reproduce, or tolimit insect-related damage or loss in crop plants or to protect theyield potential of a crop when grown in the presence of insect pests. To“control” insects may or may not mean killing the insects, although itpreferably means killing the insects.

The terms “comprises” and/or “comprising,” when used in thisspecification, specify the presence of stated features, integers, steps,operations, elements, and/or components, but do not preclude thepresence or addition of one or more other features, integers, steps,operations, elements, components, and/or groups thereof.

As used herein, the transitional phrase “consisting essentially of” (andgrammatical variants) means that the scope of a claim is to beinterpreted to encompass the specified materials or steps recited in theclaim” and those that do not materially alter the basic and novelcharacteristic(s)” of the claimed invention. Thus, the term “consistingessentially of” when used in a claim of this invention is not intendedto be interpreted to be equivalent to “comprising.”

In the context of the invention, “corresponding to” or “corresponds to”means that when the amino acid sequences of variant Cry proteins arealigned with each other, the amino acids that “correspond to” certainenumerated positions in the variant or homolog protein are those thatalign with these positions in a reference protein but that are notnecessarily in these exact numerical positions relative to theparticular reference amino acid sequence of the invention. For example,if SEQ ID NO:16 is the reference sequence and is aligned with SEQ IDNO:17, the Ala150 of SEQ ID NO:17 “corresponds to” Ala163 of SEQ IDNO:16.

To “deliver” a composition or toxic protein means that the compositionor toxic protein comes in contact with an insect, resulting in a toxiceffect and control of the insect. The composition or toxic protein canbe delivered in many recognized ways, e.g., orally by ingestion by theinsect or by contact with the insect via transgenic plant expression,formulated protein composition(s), sprayable protein composition(s), abait matrix, or any other art-recognized protein delivery system.

The term “domain” refers to a set of amino acids conserved at specificpositions along an alignment of sequences of evolutionarily relatedproteins. While amino acids at other positions can vary betweenhomologues, amino acids that are highly conserved at specific positionsindicate amino acids that are likely essential in the structure,stability or function of a protein. Identified by their high degree ofconservation in aligned sequences of a family of protein homologues,they can be used as identifiers to determine if any polypeptide inquestion belongs to a previously identified polypeptide family.

“Effective insect-controlling amount” means that concentration of toxicprotein that inhibits, through a toxic effect, the ability of insects tosurvive, grow, feed and/or reproduce, or to limit insect-related damageor loss in crop plants or protects the yield potential of a crop whengrown in the presence of insect pests. “Effective insect-controllingamount” may or may not mean killing the insects, although it preferablymeans killing the insects.

“Expression cassette” as used herein means a nucleic acid moleculecapable of directing expression of at least one polynucleotide ofinterest in an appropriate host cell, comprising a promoter operablylinked to the polynucleotide of interest which is operably linked to atermination signal. An “expression cassette” also typically comprisesadditional polynucleotides required for proper translation of thepolynucleotide of interest. The expression cassette may also compriseother polynucleotides not necessary in the direct expression of apolynucleotide of interest but which are present due to convenientrestriction sites for removal of the cassette from an expression vector.The expression cassette comprising the polynucleotide(s) of interest maybe chimeric, meaning that at least one of its components is heterologouswith respect to at least one of its other components. The expressioncassette may also be one that is naturally occurring but has beenobtained in a recombinant form useful for heterologous expression.Typically, however, the expression cassette is heterologous with respectto the host, i.e. the polynucleotide of interest in the expressioncassette does not occur naturally in the host cell and must have beenintroduced into the host cell or an ancestor of the host cell by atransformation process or a breeding process. The expression of thepolynucleotide(s) of interest in the expression cassette is generallyunder the control of a promoter. In the case of a multicellularorganism, such as a plant, the promoter can also be specific orpreferential to a particular tissue, or organ, or stage of development.An expression cassette, or fragment thereof, can also be referred to as“inserted polynucleotide” or “insertion polynucleotide” when transformedinto a plant.

A “gene” is defined herein as a hereditary unit consisting of apolynucleotide that occupies a specific location on a chromosome orplasmid and that contains the genetic instruction for a particularcharacteristic or trait in an organism.

A “gut protease” is a protease naturally found in the digestive tract ofan insect. This protease is usually involved in the digestion ofingested proteins.

The term “heterologous” when used in reference to a gene or nucleic acidrefers to a gene encoding a factor that is not in its naturalenvironment (i.e., has been altered by the hand of man). For example, aheterologous gene may include a gene from one species introduced intoanother species. A heterologous gene may also include a gene native toan organism that has been altered in some way (e.g., mutated, added inmultiple copies, linked to a non-native promoter or enhancerpolynucleotide, etc.). Heterologous genes further may comprise plantgene polynucleotides that comprise cDNA forms of a plant gene; the cDNAsmay be expressed in either a sense (to produce mRNA) or anti-senseorientation (to produce an anti-sense RNA transcript that iscomplementary to the mRNA transcript). In one aspect of the invention,heterologous genes are distinguished from endogenous plant genes in thatthe heterologous gene polynucleotide are typically joined topolynucleotides comprising regulatory elements such as promoters thatare not found naturally associated with the gene for the protein encodedby the heterologous gene or with plant gene polynucleotide in thechromosome, or are associated with portions of the chromosome not foundin nature (e.g., genes expressed in loci where the gene is not normallyexpressed). Further, a “heterologous” polynucleotide refers to apolynucleotide not naturally associated with a host cell into which itis introduced, including non-naturally occurring multiple copies of anaturally occurring polynucleotide.

“Homologous recombination” is the exchange (“crossing over”) of DNAfragments between two DNA molecules or chromatids of paired chromosomesin a region of identical polynucleotides. A “recombination event” isherein understood to mean a meiotic crossing-over.

A nucleic acid sequence is “isocoding” with a reference nucleic acidsequence when the nucleic acid sequence encodes a polypeptide having thesame amino acid sequence as the polypeptide encoded by the referencenucleic acid sequence.

The term “isolated” nucleic acid molecule, polynucleotide or toxin is anucleic acid molecule, polynucleotide or toxic protein that no longerexists in its natural environment. An isolated nucleic acid molecule,polynucleotide or toxin of the invention may exist in a purified form ormay exist in a recombinant host such as in a transgenic bacterial cellor a transgenic plant.

A “nucleic acid molecule” is single- or double-stranded DNA or RNA thatcan be isolated from any source. In the context of the presentinvention, the nucleic acid molecule is preferably a segment of DNA.

“Operably linked” refers to the association of polynucleotides on asingle nucleic acid fragment so that the function of one affects thefunction of the other. For example, a promoter is operably linked with acoding polynucleotide or functional RNA when it is capable of affectingthe expression of that coding polynucleotide or functional RNA (i.e.,that the coding polynucleotide or functional RNA is under thetranscriptional control of the promoter). Coding polynucleotide in senseor antisense orientation can be operably linked to regulatorypolynucleotides.

As used herein “pesticidal,” insecticidal,” and the like, refer to theability of a Cry protein of the invention to control a pest organism oran amount of a Cry protein that can control a pest organism as definedherein. Thus, a pesticidal Cry protein can kill or inhibit the abilityof a pest organism (e.g., insect pest) to survive, grow, feed, and/orreproduce.

A “plant” is any plant at any stage of development, particularly a seedplant.

A “plant cell” is a structural and physiological unit of a plant,comprising a protoplast and a cell wall. The plant cell may be in theform of an isolated single cell or a cultured cell, or as a part of ahigher organized unit such as, for example, plant tissue, a plant organ,or a whole plant.

“Plant cell culture” means cultures of plant units such as, for example,protoplasts, cell culture cells, cells in plant tissues, pollen, pollentubes, ovules, embryo sacs, zygotes and embryos at various stages ofdevelopment.

“Plant material” refers to leaves, stems, roots, flowers or flowerparts, fruits, pollen, egg cells, zygotes, seeds, cuttings, cell ortissue cultures, or any other part or product of a plant.

A “plant organ” is a distinct and visibly structured and differentiatedpart of a plant such as a root, stem, leaf, flower bud, or embryo.

“Plant tissue” as used herein means a group of plant cells organizedinto a structural and functional unit. Any tissue of a plant in plantaor in culture is included. This term includes, but is not limited to,whole plants, plant organs, plant seeds, tissue culture and any groupsof plant cells organized into structural and/or functional units. Theuse of this term in conjunction with, or in the absence of, any specifictype of plant tissue as listed above or otherwise embraced by thisdefinition is not intended to be exclusive of any other type of planttissue.

A “polynucleotide” refers to a polymer composed of many nucleotidemonomers covalently bonded in a chain. Such “polynucleotides” includesDNA, RNA, modified oligo nucleotides (e.g., oligonucleotides comprisingbases that are not typical to biological RNA or DNA, such as2′-O-methylated oligonucleotides), and the like. In some embodiments, anucleic acid or polynucleotide can be single-stranded, double-stranded,multi-stranded, or combinations thereof. Unless otherwise indicated, aparticular nucleic acid or polynucleotide of the present inventionoptionally comprises or encodes complementary polynucleotides, inaddition to any polynucleotide explicitly indicated.

“Polynucleotide of interest” refers to any polynucleotide which, whentransferred to an organism, e.g. a plant, confers upon the organism adesired characteristic such as antibiotic resistance, virus resistance,insect resistance, disease resistance, or resistance to other pests,herbicide tolerance, improved nutritional value, improved performance inan industrial process, production of commercially valuable enzymes ormetabolites or altered reproductive capability.

The term “promoter” refers to a polynucleotide, usually upstream (5′) ofits coding polynucleotide, which controls the expression of the codingpolynucleotide by providing the recognition for RNA polymerase and otherfactors required for proper transcription.

A “protoplast” is an isolated plant cell without a cell wall or withonly parts of the cell wall.

As used herein, the term “recombinant” refers to a form of nucleic acid(e.g. DNA or RNA) and/or protein and/or an organism that would notnormally be found in nature and as such was created by humanintervention. As used herein, a “recombinant nucleic acid molecule” is anucleic acid molecule comprising a combination of polynucleotides thatwould not naturally occur together and is the result of humanintervention, e.g., a nucleic acid molecule that is comprised of acombination of at least two polynucleotides heterologous to each other,and/or a nucleic acid molecule that is artificially synthesized andcomprises a polynucleotide that deviates from the polynucleotide thatwould normally exist in nature, and/or a nucleic acid molecule thatcomprises a transgene artificially incorporated into a host cell'sgenomic DNA and the associated flanking DNA of the host cell's genome.An example of a recombinant nucleic acid molecule is a DNA moleculeresulting from the insertion of a transgene into a plant's genomic DNA,which may ultimately result in the expression of a recombinant RNAand/or protein molecule in that organism. As used herein, a “recombinantplant” is a plant that would not normally exist in nature, is the resultof human intervention, and contains a transgene and/or heterologousnucleic acid molecule incorporated into its genome. As a result of suchgenomic alteration, the recombinant plant is distinctly different fromthe related wild-type plant.

“Regulatory elements” refer to sequences involved in controlling theexpression of a nucleotide sequence. Regulatory elements comprise apromoter operably linked to the nucleotide sequence of interest andtermination signals. They also typically encompass sequences requiredfor proper translation of the nucleotide sequence.

The term “identical” or “substantially identical,” in the context of twonucleic acid or protein sequences, refers to two or more sequences orsubsequences that have at least 60%, preferably 80%, more preferably 90,even more preferably 95%, and most preferably at least 99% nucleotide oramino acid residue identity, when compared and aligned for maximumcorrespondence, as measured using one of the following sequencecomparison algorithms or by visual inspection. Preferably, thesubstantial identity exists over a region of the sequences that is atleast about 50 residues in length, more preferably over a region of atleast about 100 residues, and most preferably the sequences aresubstantially identical over at least about 150 residues. In anespecially preferred embodiment, the sequences are substantiallyidentical over the entire length of the coding regions. Furthermore,substantially identical nucleic acid or protein sequences performsubstantially the same function.

For sequence comparison, typically one sequence acts as a referencesequence to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are input into acomputer, subsequence coordinates are designated if necessary, andsequence algorithm program parameters are designated. The sequencecomparison algorithm then calculates the percent sequence identity forthe test sequence(s) relative to the reference sequence, based on thedesignated program parameters.

Optimal alignment of sequences for comparison can be conducted, e.g., bythe local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch,J. Mol. Biol. 48: 443 (1970), by the search for similarity method ofPearson & Lipman, Proc. Nat'l. Acad Sci. USA 85: 2444 (1988), bycomputerized implementations of these algorithms (GAP, BESTFIT, FASTA,and TFASTA in the Wisconsin Genetics Software Package, Genetics ComputerGroup, 575 Science Dr., Madison, Wis.), or by visual inspection (seegenerally, Ausubel et al., infra).

One example of an algorithm that is suitable for determining percentsequence identity and sequence similarity is the BLAST algorithm, whichis described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990).Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information (National Center forBiotechnology Information, U.S. National Library of Medicine, 8600Rockville Pike, Bethesda, Md. 20894 USA). This algorithm involves firstidentifying high scoring sequence pairs (HSPs) by identifying shortwords of length W in the query sequence, which either match or satisfysome positive-valued threshold score T when aligned with a word of thesame length in a database sequence. T is referred to as the neighborhoodword score threshold (Altschul et al., 1990). These initial neighborhoodword hits act as seeds for initiating searches to find longer HSPscontaining them. The word hits are then extended in both directionsalong each sequence for as far as the cumulative alignment score can beincreased. Cumulative scores are calculated using, for nucleotidesequences, the parameters M (reward score for a pair of matchingresidues; always>0) and N (penalty score for mismatching residues;always<0). For amino acid sequences, a scoring matrix is used tocalculate the cumulative score. Extension of the word hits in eachdirection are halted when the cumulative alignment score falls off bythe quantity X from its maximum achieved value, the cumulative scoregoes to zero or below due to the accumulation of one or morenegative-scoring residue alignments, or the end of either sequence isreached. The BLAST algorithm parameters W, T, and X determine thesensitivity and speed of the alignment. The BLASTN program (fornucleotide sequences) uses as defaults a wordlength (W) of 11, anexpectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison ofboth strands. For amino acid sequences, the BLASTP program uses asdefaults a wordlength (W) of 3, an expectation (E) of 10, and theBLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad Sci.USA 89: 10915 (1989)).

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA90: 5873-5787 (1993)). One measure of similarity provided by the BLASTalgorithm is the smallest sum probability (P(N)), which provides anindication of the probability by which a match between two nucleotide oramino acid sequences would occur by chance. For example, a test nucleicacid sequence is considered similar to a reference sequence if thesmallest sum probability in a comparison of the test nucleic acidsequence to the reference nucleic acid sequence is less than about 0.1,more preferably less than about 0.01, and most preferably less thanabout 0.001.

Another indication that two nucleic acid sequences are substantiallyidentical is that the two molecules hybridize to each other understringent conditions. The phrase “hybridizing specifically to” refers tothe binding, duplexing, or hybridizing of a molecule only to aparticular nucleotide sequence under stringent conditions when thatsequence is present in a complex mixture (e.g., total cellular) DNA orRNA. “Bind(s) substantially” refers to complementary hybridizationbetween a probe nucleic acid and a target nucleic acid and embracesminor mismatches that can be accommodated by reducing the stringency ofthe hybridization media to achieve the desired detection of the targetnucleic acid sequence.

“Stringent hybridization conditions” and “stringent hybridization washconditions” in the context of nucleic acid hybridization experimentssuch as Southern and Northern hybridizations are sequence dependent, andare different under different environmental parameters. Longer sequenceshybridize specifically at higher temperatures. An extensive guide to thehybridization of nucleic acids is found in Tijssen (1993) LaboratoryTechniques in Biochemistry and Molecular Biology-Hybridization withNucleic Acid Probes part I chapter 2 “Overview of principles ofhybridization and the strategy of nucleic acid probe assays” Elsevier,N.Y. Generally, highly stringent hybridization and wash conditions areselected to be about 5° C. lower than the thermal melting point (T_(m))for the specific sequence at a defined ionic strength and pH. Typically,under “stringent conditions” a probe will hybridize to its targetsubsequence, but not to other sequences.

The T_(m) is the temperature (under defined ionic strength and pH) atwhich 50% of the target sequence hybridizes to a perfectly matchedprobe. Very stringent conditions are selected to be equal to the T_(m)for a particular probe. An example of stringent hybridization conditionsfor hybridization of complementary nucleic acids which have more than100 complementary residues on a filter in a Southern or northern blot is50% formamide with 1 mg of heparin at 42° C., with the hybridizationbeing carried out overnight. An example of highly stringent washconditions is 0.15M NaCl at 72° C. for about 15 minutes. An example ofstringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes(see, Sambrook, infra, for a description of SSC buffer). Often, a highstringency wash is preceded by a low stringency wash to removebackground probe signal. An example medium stringency wash for a duplexof, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes.An example low stringency wash for a duplex of, e.g., more than 100nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes(e.g., about 10 to 50 nucleotides), stringent conditions typicallyinvolve salt concentrations of less than about 1.0 M Na ion, typicallyabout 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to8.3, and the temperature is typically at least about 30° C. Stringentconditions can also be achieved with the addition of destabilizingagents such as formamide. In general, a signal to noise ratio of 2× (orhigher) than that observed for an unrelated probe in the particularhybridization assay indicates detection of a specific hybridization.Nucleic acids that do not hybridize to each other under stringentconditions are still substantially identical if the proteins that theyencode are substantially identical. This occurs, e.g., when a copy of anucleic acid is created using the maximum codon degeneracy permitted bythe genetic code.

The following are examples of sets of hybridization/wash conditions thatmay be used to clone homologous nucleotide sequences that aresubstantially identical to reference nucleotide sequences of the presentinvention: a reference nucleotide sequence preferably hybridizes to thereference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 MNaPO₄, 1 mM EDTA at 50° C. with washing in 2×SSC, 0.1% SDS at 50° C.,more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mMEDTA at 50° C. with washing in 1×SSC, 0.1% SDS at 50° C., more desirablystill in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50°C. with washing in 0.5×SSC, 0.1% SDS at 50° C., preferably in 7% sodiumdodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in0.1×SSC, 0.1% SDS at 50° C., more preferably in 7% sodium dodecylsulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC,0.1% SDS at 65° C.

A further indication that two nucleic acid sequences or proteins aresubstantially identical is that the protein encoded by the first nucleicacid is immunologically cross reactive with, or specifically binds to,the protein encoded by the second nucleic acid. Thus, a protein istypically substantially identical to a second protein, for example,where the two proteins differ only by conservative substitutions.

“Synthetic” refers to a nucleotide sequence comprising bases and/orstructural features that are not present in the natural sequence. Forexample, an artificial sequence encoding a Cry protein of the inventionthat resembles more closely the G+C content and the normal codondistribution of dicot and/or monocot plant genes is said to besynthetic.

“Transformation” is a process for introducing heterologous nucleic acidinto a host cell or organism. In particular, “transformation” means thestable integration of a DNA molecule into the genome of an organism ofinterest.

“Transformed/transgenic/recombinant” refer to a host organism such as abacterium or a plant into which a heterologous nucleic acid molecule hasbeen introduced. The nucleic acid molecule can be stably integrated intothe genome of the host or the nucleic acid molecule can also be presentas an extrachromosomal molecule. Such an extrachromosomal molecule canbe auto-replicating. Transformed cells, tissues, or plants areunderstood to encompass not only the end product of a transformationprocess, but also transgenic progeny thereof. A “non-transformed”,“non-transgenic”, or “non-recombinant” host refers to a wild-typeorganism, e.g., a bacterium or plant, which does not contain theheterologous nucleic acid molecule.

Nucleotides are indicated by their bases by the following standardabbreviations: adenine (A), cytosine (C), thymine (T), and guanine (G).Amino acids are likewise indicated by the following standardabbreviations: alanine (Ala; A), arginine (Arg; R), asparagine (Asn; N),aspartic acid (Asp; D), cysteine (Cys; C), glutamine (Gln; Q), glutamicacid (Glu; E), glycine (Gly; G), histidine (His; H), isoleucine (Ile;l), leucine (Leu; L), lysine (Lys; K), methionine (Met; M),phenylalanine (Phe; F), proline (Pro; P), serine (Ser; S), threonine(Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y), and valine (Val; V).

This invention provides compositions and methods for controlling harmfulplant pests. Particularly, the invention relates to Cry proteins thatare toxic to plant pests and to polynucleotides that comprise nucleotidesequences that encode the Cry proteins, and to the making and using ofthe polynucleotides and Cry proteins to control plant pests.

Accordingly, in some embodiments, a chimeric gene is provided thatcomprises a heterologous promoter operably linked to a polynucleotidecomprising a nucleotide sequence that encodes a protein toxic to atleast European corn borer (Ostrinia nubilalis), wherein the nucleotidesequence (a) has at least 80% (e.g. 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%,99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%) to at least 99%(99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%)sequence identity with any one of SEQ ID NOs:1-5; or (b) encodes aprotein comprising an amino acid sequence that has at least 80% (e.g.80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%,99.7%, 99.8%, 99.9%) to at least 99% (99%, 99.1%, 99.2%, 99.3%, 99.4%,99.5%, 99.6%, 99.7%, 99.8%, 99.9%) sequence identity with any one of SEQID NOs:16-20; or (c) is a synthetic sequence of (a) or (b) that hascodons optimized for expression in a transgenic organism.

In other embodiments, the heterologous promoter is a plant-expressiblepromoter. For example, without limitation, the plant-expressiblepromoter can be selected from the group consisting of ubiquitin, cmp,corn TrpA, bacteriophage T3 gene 9 5′ UTR, corn sucrose synthetase 1,corn alcohol dehydrogenase 1, corn light harvesting complex, corn heatshock protein, pea small subunit RuBP carboxylase, Ti plasmid mannopinesynthase, Ti plasmid nopaline synthase, petunia chalcone isomerase, beanglycine rich protein 1, Potato patatin, lectin, CaMV 35S, and the S-E9small subunit RuBP carboxylase promoter.

In additional embodiments, the protein encoded by the chimeric gene isadditionally toxic to one or more insect species selected from the groupconsisting of black cutworm (Agrotis ipsilon), fall armyworm (Spodopterafrugiperda), corn earworm (Helicoverpa zea), sugarcane borer (Diatraeasaccharalis), velvetbean caterpillar (Anticarsia gemmatalis), soybeanlooper (Chrysodeixis includes), southwest corn borer (Diatraeagrandiosella), western bean cutworm (Richia albicosta), tobacco budworm(Heliothis virescens), Asian corn borer (Ostrinia furnacalis), cottonbollworm (Helicoverpa armigera), striped stein borer (Chilosuppressalis), pink stein borer (Sesamia calamistis) and rice leaffolder(Cnaphalocrocis medinalis).

In further embodiments, the polynucleotide comprises a nucleotidesequence that has at least 80% to at least 99% sequence identity withSEQ ID NO:1, or has at least 80% to at least 99% sequence identity withSEQ ID NO:2, or has at least 80% to at least 99% sequence identity withSEQ ID NO:3, or has at least 80% to at least 99% sequence identity withSEQ ID NO:4, or has at least 80% to at least 99% sequence identity withSEQ ID NO:5.

In other embodiments, the polynucleotide comprises a nucleotide sequencethat encodes a protein comprising an amino acid sequence that has atleast 80% to at least 99% sequence identity with any one of SEQ IDNOS:16-20.

In still other embodiments, the amino acid sequence has at least 90%, orat least 91%, or at least 92%, or at least 94%, or at least 94%, or atleast 95%, or at least 96%, or at least 97%, or at least 98%, or atleast 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, orat least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%,or at least 99.8%, or at least 99.9% sequence identity with SEQ IDNO:16.

In further embodiments, the amino acid sequence has at least 99%, or atleast 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, orat least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%,or at least 99.9% sequence identity with SEQ ID NO:17.

In still further embodiments, the amino acid sequence has at least 99%,or at least 99.1%, or at least 99.2%, or at least 99.3%, or at least99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%, or atleast 99.8%, or at least 99.9% sequence identity with SEQ ID NO:18.

In other embodiments, the amino acid sequence has at least 90%, or atleast 91%, or at least 92%, or at least 94%, or at least 94%, or atleast 95%, or at least 96%, or at least 97%, or at least 98%, or atleast 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, orat least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%,or at least 99.8%, or at least 99.9% sequence identity with SEQ IDNO:19.

In still other embodiments, the amino acid sequence has at least 80%, orat least 81%, or at least 82%, or at least 83%, or at least 84%, or atleast 85%, or at least 86%, or at least 87%, or at least 88%, or atleast 89%, or at least 90%, or at least 91%, or at least 92%, or atleast 94%, or at least 94%, or at least 95%, or at least 96%, or atleast 97%, or at least 98%, or at least 99%, or at least 99.1%, or atleast 99.2%, or at least 99.3%, or at least 99.4%, or at least 99.5% orat least 99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9%sequence identity with SEQ ID NO:20.

In some embodiments, the chimeric gene of the invention comprises apolynucleotide comprising a synthetic sequence of a nucleotide sequencethat has at least 80%, or at least 81%, or at least 82%, or at least83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%,or at least 88%, or at least 89%, or at least 90%, or at least 91%, orat least 92%, or at least 94%, or at least 94%, or at least 95%, or atleast 96%, or at least 97%, or at least 98%, or at least 99%, or atleast 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, orat least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%,or at least 99.9% with any of SEQ ID NOS:6-15, wherein the syntheticsequence has codons optimized for expression is a transgenic organism.In other embodiments, the chimeric gene of the invention comprises apolynucleotide comprising a synthetic sequence of a nucleotide sequencethat encodes a protein comprising an amino acid sequence that has atleast 80%, or at least 81%, or at least 82%, or at least 83%, or atleast 84%, or at least 85%, or at least 86%, or at least 87%, or atleast 88%, or at least 89%, or at least 90%, or at least 91%, or atleast 92%, or at least 94%, or at least 94%, or at least 95%, or atleast 96%, or at least 97%, or at least 98%, or at least 99%, or atleast 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, orat least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%,or at least 99.9% sequence identity with any of SEQ ID NOS:16-25,wherein the synthetic sequence has codons optimized for expression is atransgenic organism. In further embodiments, the transgenic organism isa transgenic bacteria or a transgenic plant.

In some embodiments, the invention provides a synthetic polynucleotidecomprising, consisting essentially of or consisting of a nucleotidesequence that encodes a protein that is active against at least Europeancorn borer (Ostrinia nubilalis), wherein the nucleotide sequence has atleast 80%, or at least 81%, or at least 82%, or at least 83%, or atleast 84%, or at least 85%, or at least 86%, or at least 87%, or atleast 88%, or at least 89%, or at least 90%, or at least 91%, or atleast 92%, or at least 94%, or at least 94%, or at least 95%, or atleast 96%, or at least 97%, or at least 98%, or at least 99%, or atleast 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, orat least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%,or at least 99.9% sequence identity with any one of SEQ ID NOS:6-15.

In other embodiments, the invention provides a synthetic polynucleotidecomprising, consisting essentially of or consisting of a nucleotidesequence that encodes a protein that is active against at least Europeancorn borer (Ostrinia nubilalis), wherein the nucleotide sequence encodesan amino acid sequence that has at least 80%, or at least 81%, or atleast 82%, or at least 83%, or at least 84%, or at least 85%, or atleast 86%, or at least 87%, or at least 88%, or at least 89%, or atleast 90%, or at least 91%, or at least 92%, or at least 94%, or atleast 94%, or at least 95%, or at least 96%, or at least 97%, or atleast 98%, or at least 99%, or at least 99.1%, or at least 99.2%, or atleast 99.3%, or at least 99.4%, or at least 99.5% or at least 99.6%, orat least 99.7%, or at least 99.8%, or at least 99.9% sequence identitywith any one of SEQ ID NOS:16-25.

According to some embodiments, the invention provides an isolatedprotein that is toxic to at least European corn borer (Ostrinianubilalis), wherein the protein comprises, consists essentially of orconsists of (a) an amino acid sequence that has at least 80% sequenceidentity to at least 99% sequence identity with an amino acid sequencerepresented by any one of SEQ ID NOs:16-25 or (b) an amino acid sequencethat is encoded by a nucleotide sequence that has at least 80% sequenceidentity to at least 99% sequence identity with a nucleotide sequencerepresented by any one of SEQ ID NOs:6-15.

In other embodiments, the isolated protein comprises, consistsessentially of or consists of an amino acid sequence that has at least80% to at least 99% sequence identity with any one of SEQ ID NOS:16-20.In still other embodiments, the amino acid sequence has at least 90%, orat least 91%, or at least 92%, or at least 94%, or at least 94%, or atleast 95%, or at least 96%, or at least 97%, or at least 98%, or atleast 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, orat least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%,or at least 99.8%, or at least 99.9% sequence identity with SEQ IDNO:16.

In other embodiments, the amino acid sequence has at least 99%, or atleast 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, orat least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%,or at least 99.9% sequence identity with SEQ ID NO:17.

In further embodiments, the amino acid sequence has at least 99%, or atleast 99.1%, or at least 99.2%, or at least 99.3%, or at least 99.4%, orat least 99.5% or at least 99.6%, or at least 99.7%, or at least 99.8%,or at least 99.9% sequence identity with SEQ ID NO:18.

In still further embodiments, the amino acid sequence has at least 90%,or at least 91%, or at least 92%, or at least 94%, or at least 94%, orat least 95%, or at least 96%, or at least 97%, or at least 98%, or atleast 99%, or at least 99.1%, or at least 99.2%, or at least 99.3%, orat least 99.4%, or at least 99.5% or at least 99.6%, or at least 99.7%,or at least 99.8%, or at least 99.9% sequence identity with SEQ IDNO:19.

In still other embodiments, the amino acid sequence has at least 80%, orat least 81%, or at least 82%, or at least 83%, or at least 84%, or atleast 85%, or at least 86%, or at least 87%, or at least 88%, or atleast 89%at least 90%, or at least 91%, or at least 92%, or at least94%, or at least 94%, or at least 95%, or at least 96%, or at least 97%,or at least 98%, or at least 99%, or at least 99.1%, or at least 99.2%,or at least 99.3%, or at least 99.4%, or at least 99.5% or at least99.6%, or at least 99.7%, or at least 99.8%, or at least 99.9% sequenceidentity with SEQ ID NO:20.

In some embodiments, the amino acid sequence comprises, consistsessentially of or consists of any one of SEQ ID NOs:16-25.

Antibodies raised in response to immune challenge by a native or mutantBT-0009, BT-0012, BT-0013, BT-0023 and BT-0067 and the like or relatedproteins of the present invention may be produced using standardimmunological techniques for production of polyclonal antisera and, ifdesired, immortalizing the antibody-producing cells of the immunizedhost for sources of monoclonal antibody production. Techniques forproducing antibodies to any substance of interest are well known, e.g.,as in Harlow and Lane (1988) and as in Goding (1986). The presentinvention encompasses insecticidal proteins that cross-react withantibodies raised against one or more of the insecticidal Cry proteinsof the present invention.

The antibodies produced in the present invention are also useful inimmunoassays for determining the amount or presence of a native ormutant BT-0044, BT-0051, BT-0068 and BT-0128 or related protein in abiological sample. Such assays are also useful in quality-controlledproduction of compositions containing one or more of the toxic proteinsof the present invention or related toxic proteins. In addition, theantibodies can be used to assess the efficacy of recombinant productionof one or more of the proteins of the present invention or a relatedprotein, as well as for screening expression libraries for the presenceof a nucleotide sequence encoding one or more of the proteins of theinvention or related protein coding sequences. Antibodies are usefulalso as affinity ligands for purifying and/or isolating any one or moreof the proteins of the present invention and related proteins. Theproteins of the present invention and proteins containing relatedantigenic epitopes may be obtained by over expressing full or partiallengths of a sequence encoding all or part of a protein of the presentinvention or a related protein in a preferred host cell.

It is recognized that DNA sequences that encode a native Cry protein ofthe invention may be altered by various methods, and that thesealterations may result in DNA sequences encoding proteins with aminoacid sequences different than that encoded by a native Cry protein ofthe invention. This protein may be altered in various ways includingamino acid substitutions, deletions, truncations, and insertions of oneor more amino acids of any of SEQ ID NOs:13-16, including up to about 2,about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10,about 15, about 20, about 25, about 30, about 35, about 40, about 45,about 50, about 55, about 60, about 65, about 70, about 75, about 80,about 85, about 90, about 100, about 105, about 110, about 115, about120, about 125, about 130, about 135, about 140, about 145, about 150,about 155, or more amino acid substitutions, deletions or insertions.Methods for such manipulations are generally known in the art. Forexample, amino acid sequence variants of a native Cry protein can beprepared by mutations in a polynucleotide that encodes the protein. Thismay also be accomplished by one of several forms of mutagenesis and/orin directed evolution. In some aspects, the changes encoded in the aminoacid sequence will not substantially affect the function of the protein.Such variants will possess the desired insecticidal activity. In oneembodiment of the invention, nucleotide sequences represented by SEQ IDNOs: 1-5 are altered to introduce amino acid substitutions in theencoded protein. In some embodiments, the resulting mutant protein isencoded by a synthetic mutant polynucleotide comprising a nucleotidesequence represented by any one of SEQ ID NOs:11-15. In otherembodiments, the mutant proteins comprise, consist essentially of orconsist of an amino acid sequence represented by any one of SEQ IDNOs:21-25.

It is understood that the ability of an insecticidal protein to conferinsecticidal activity may be improved by the use of such techniques uponthe compositions of this invention. For example, one may express a Cryprotein in host cells that exhibit high rates of base misincorporationduring DNA replication, such as XL-1 Red (Stratagene, La Jolla, Calif.).After propagation in such strains, one can isolate the DNA (for exampleby preparing plasmid DNA, or by amplifying by PCR and cloning theresulting PCR fragment into a vector), culture the Cry protein mutationsin a non-mutagenic strain, and identify mutated genes with insecticidalactivity, for example by performing an assay to test for insecticidalactivity. Generally, the protein is mixed and used in feeding assays.See, for example Marrone et al. (1985) J. of Economic Entomology78:290-293. Such assays can include contacting plants with one or morepests and determining the plant's ability to survive and/or cause thedeath of the pests. Examples of mutations that result in increasedtoxicity are found in Schnepf et al. (1998) Microbiol. Mol. Biol. Rev.62:775-806.

Alternatively, alterations may be made to an amino acid sequence of theinvention at the amino or carboxy terminus without substantiallyaffecting activity. This can include insertions, deletions, oralterations introduced by modern molecular methods, such as PCR,including PCR amplifications that alter or extend the protein codingsequence by virtue of inclusion of amino acid encoding sequences in theoligonucleotides utilized in the PCR amplification. Alternatively, theprotein sequences added can include entire protein-coding sequences,such as those used commonly in the art to generate protein fusions. Suchfusion proteins are often used to (1) increase expression of a proteinof interest (2) introduce a binding domain, enzymatic activity, orepitope to facilitate either protein purification, protein detection, orother experimental uses known in the art (3) target secretion ortranslation of a protein to a subcellular organelle, such as theperiplasmic space of Gram-negative bacteria, or the endoplasmicreticulum of eukaryotic cells, the latter of which often results inglycosylation of the protein.

A Cry protein of the invention can also be mutated to introduce anepitope to generate antibodies that recognize the mutated protein.Therefore, in some embodiments, the invention provides a mutated Cryprotein, wherein an amino acid substitution in a native Cry proteinproduces a mutant Cry protein having an antigenic region that allows themutant Cry protein to be distinguished from the native Cry protein in aprotein detection assay.

In some embodiments, the invention provides a method of making anantibody that differentially recognizes a mutated Cry protein from thenative Cry protein from which the mutated Cry protein is derived, themethod comprising the steps of substituting amino acids in an antigenicloop of a native Cry protein and raising antibodies that specificallyrecognize the mutated antigenic loop in the mutated Cry protein and doesnot recognize the native Cry protein. In one embodiment, the antigenicloop is identified in non-conserved regions outside of domain I of thenative Cry protein. In another embodiment, the antigenic loop is not aloop involved in the Cry protein's insect gut receptor recognition orinvolved in the protease activation of the Cry protein.

Variant nucleotide and amino acid sequences of the present inventionalso encompass sequences derived from mutagenic and recombinogenicprocedures such as DNA shuffling. With such a procedure, one or moredifferent toxic protein coding regions can be used to create a new toxicprotein possessing the desired properties. In this manner, libraries ofrecombinant polynucleotides are generated from a population of relatedsequence polynucleotides comprising sequence regions that havesubstantial sequence identity and can be homologously recombined invitro or in vivo. For example, using this approach, sequence motifsencoding a domain of interest may be shuffled between a pesticidal geneof the invention and other known pesticidal genes to obtain a new genecoding for a protein with an improved property of interest, such as anincreased insecticidal activity. Strategies for such DNA shuffling areknown in the art. See, for example, Stemmer (1994) Proc. Natl. Acad.Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri etal. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol.272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat.Nos. 5,605,793 and 5,837,458.

Domain swapping or shuffling is another mechanism for generating alteredCry proteins of the invention. Domains may be swapped between Cryproteins, resulting in hybrid or chimeric toxic proteins with improvedpesticidal activity or target spectrum. Methods for generatingrecombinant proteins and testing them for pesticidal activity are wellknown in the art (see, for example, Naimov et al. (2001) Appl. Environ.Microbiol. 67:5328-5330; de Maagd et al. (1996) Appl. Environ.Microbiol. 62:1537-1543; Ge et al. (1991) J. Biol. Chem.266:17954-17958; Schnepf et al. (1990) J. Biol. Chem. 265:20923-20930;Rang et al. 91999) Appl. Environ. Microbiol. 65:2918-2925).

In some embodiments, the invention provides a recombinant vectorcomprising a polynucleotide, a nucleic acid molecule, an expressioncassette or a chimeric gene of the invention. In other embodiments, thevector is further defined as a plasmid, cosmid, phagemid, artificialchromosome, phage or viral vector. Certain vectors for use intransformation of plants and other organisms are known in the art.

Thus, some embodiments of the invention are directed to expressioncassettes designed to express the polynucleotides and nucleic acidmolecules of the invention. As used herein, “expression cassette” meansa nucleic acid molecule having at least a control sequence operativelylinked to a nucleotide sequence of interest. In this manner, forexample, plant promoters operably linked to the nucleotide sequences tobe expressed are provided in expression cassettes for expression in aplant, plant part and/or plant cell.

An expression cassette comprising a nucleotide sequence of interest maybe chimeric, meaning that at least one of its components is heterologouswith respect to at least one of its other components. An expressioncassette may also be one that is naturally occurring but has beenobtained in a recombinant form useful for heterologous expression.Typically, however, the expression cassette is heterologous with respectto the host, i.e., the particular nucleic acid sequence of theexpression cassette does not occur naturally in the host cell and musthave been introduced into the host cell or an ancestor of the host cellby a transformation event.

In addition to the promoters operatively linked to the nucleotidesequences of the invention, an expression cassette of this inventionalso can include other regulatory sequences. As used herein, “regulatorysequences” means nucleotide sequences located upstream (5′ non-codingsequences), within or downstream (3′ non-coding sequences) of a codingsequence, and which influence the transcription, RNA processing orstability, or translation of the associated coding sequence. Regulatorysequences include, but are not limited to, enhancers, introns,translation leader sequences, termination signals, and polyadenylationsignal sequences.

In some embodiments, an expression cassette of the invention also caninclude nucleotide sequences that encode other desired traits. Suchnucleotide sequences can be stacked with any combination of nucleotidesequences to create plants, plant parts or plant cells having thedesired phenotype. Stacked combinations can be created by any methodincluding, but not limited to, cross breeding plants by any conventionalmethodology, or by genetic transformation (i.e. molecular stacking). Ifstacked by genetically transforming the plants, the nucleotide sequencesof interest can be combined at any time and in any order. For example, atransgenic plant comprising one or more desired traits can be used asthe target to introduce further traits by subsequent transformation. Theadditional nucleotide sequences can be introduced simultaneously in aco-transformation protocol with a nucleotide sequence, nucleic acidmolecule, nucleic acid construct, and/or composition of this invention,provided by any combination of expression cassettes. For example, if twonucleotide sequences will be introduced, they can be incorporated inseparate cassettes (trans) or can be incorporated on the same cassette(cis). Expression of polynucleotides can be driven by the same promoteror by different promoters. It is further recognized that polynucleotidescan be stacked at a desired genomic location using a site-specificrecombination system. See, e.g., Int'l Patent Application PublicationNos. WO 99/25821; WO 99/25854; WO 99/25840; WO 99/25855 and WO 99/25853.

The expression cassette also can include a coding sequence for one ormore polypeptides for agronomic traits that primarily are of benefit toa seed company, grower or grain processor. A polypeptide of interest canbe any polypeptide encoded by a nucleotide sequence of interest.Non-limiting examples of polypeptides of interest that are suitable forproduction in plants include those resulting in agronomically importanttraits such as herbicide resistance (also sometimes referred to as“herbicide tolerance”), virus resistance, bacterial pathogen resistance,insect resistance, nematode resistance, and/or fungal resistance. See,e.g., U.S. Pat. Nos. 5,569,823; 5,304,730; 5,495,071; 6,329,504; and6,337,431. The polypeptide also can be one that increases plant vigor oryield (including traits that allow a plant to grow at differenttemperatures, soil conditions and levels of sunlight and precipitation),or one that allows identification of a plant exhibiting a trait ofinterest (e.g., a selectable marker, seed coat color, etc.). Variouspolypeptides of interest, as well as methods for introducing thesepolypeptides into a plant, are described, for example, in U.S. Pat. Nos.4,761,373; 4,769,061; 4,810,648; 4,940,835; 4,975,374; 5,013,659;5,162,602; 5,276,268; 5,304,730; 5,495,071; 5,554,798; 5,561,236;5,569,823; 5,767,366; 5,879,903, 5,928,937; 6,084,155; 6,329,504 and6,337,431; as well as US Patent Publication No. 2001/0016956. See also,on the World Wide Web at lifesci.sussex.ac.uk/home/Neil_Crickmore/Bt/.

Polynucleotides conferring resistance/tolerance to an herbicide thatinhibits the growing point or meristem, such as an imidazalinone or asulfonylurea can also be suitable in some embodiments of the invention.Exemplary polynucleotides in this category code for mutant ALS and AHASenzymes as described, e.g., in U.S. Pat. Nos. 5,767,366, and 5,928,937.U.S. Pat. Nos. 4,761,373 and 5,013,659 are directed to plants resistantto various imidazalinone or sulfonamide herbicides. U.S. Pat. No.4,975,374 relates to plant cells and plants containing a nucleic acidencoding a mutant glutamine synthetase (GS) resistant to inhibition byherbicides that are known to inhibit GS, e.g., phosphinothricin andmethionine sulfoximine. U.S. Pat. No. 5,162,602 discloses plantsresistant to inhibition by cyclohexanedione and aryloxyphenoxypropanoicacid herbicides. The resistance is conferred by an altered acetylcoenzyme A carboxylase (ACCase).

Polypeptides encoded by nucleotides sequences conferring resistance toglyphosate are also suitable for the invention. See, e.g., U.S. Pat.Nos. 4,940,835 and 4,769,061. U.S. Pat. No. 5,554,798 disclosestransgenic glyphosate resistant maize plants, which resistance isconferred by an altered 5-enolpyruvyl-3-phosphoshikimate (EPSP) synthasegene.

Polynucleotides coding for resistance to phosphono compounds such asglufosinate ammonium or phosphinothricin, and pyridinoxy or phenoxypropionic acids and cyclohexones are also suitable. See, European PatentApplication No. 0 242 246. See also, U.S. Pat. Nos. 5,879,903, 5,276,268and 5,561,236.

Other suitable polynucleotides include those coding for resistance toherbicides that inhibit photosynthesis, such as a triazine and abenzonitrile (nitrilase) See, U.S. Pat. No. 4,810,648. Additionalsuitable polynucleotides coding for herbicide resistance include thosecoding for resistance to 2,2-dichloropropionic acid, sethoxydim,haloxyfop, imidazolinone herbicides, sulfonylurea herbicides,triazolopyrimidine herbicides, s-triazine herbicides and bromoxynil.Also suitable are polynucleotides conferring resistance to a protoxenzyme, or that provide enhanced resistance to plant diseases; enhancedtolerance of adverse environmental conditions (abiotic stresses)including but not limited to drought, excessive cold, excessive heat, orexcessive soil salinity or extreme acidity or alkalinity; andalterations in plant architecture or development, including changes indevelopmental timing. See, e.g., U.S. Patent Publication No.2001/0016956 and U.S. Pat. No. 6,084,155.

Additional suitable polynucleotides include those coding for pesticidal(e.g., insecticidal) polypeptides. These polypeptides may be produced inamounts sufficient to control, for example, insect pests (i.e., insectcontrolling amounts). It is recognized that the amount of production ofpesticidal polypeptide in a plant necessary to control insects or otherpests may vary depending upon the cultivar, type of pest, environmentalfactors and the like. Polynucleotides useful for additional insect orpest resistance include, for example, those that encode toxinsidentified in Bacillus organisms. Polynucleotides comprising nucleotidesequences encoding Bacillus thuringiensis (Bt) Cry proteins from severalsubspecies have been cloned and recombinant clones have been found to betoxic to lepidopteran, dipteran and coleopteran insect larvae. Examplesof such Bt insecticidal proteins include the Cry proteins such asCry1Aa, Cry1Ab, Cry1Ac, Cry1B, Cry1C, Cry1D, Cry1Ea, Cry1Fa, Cry3A,Cry9A, Cry9B, Cry9C, and the like, as well as vegetative insecticidalproteins such as Vip1, Vip2, Vip3, and the like. A full list ofBt-derived proteins can be found on the worldwide web at Bacillusthuringiensis Toxin Nomenclature Database maintained by the Universityof Sussex (see also, Crickmore et al. (1998) Microbiol. Mol. Biol. Rev.62:807-813).

Polypeptides that are suitable for production in plants further includethose that improve or otherwise facilitate the conversion of harvestedplants and/or plant parts into a commercially useful product, including,for example, increased or altered carbohydrate content and/ordistribution, improved fermentation properties, increased oil content,increased protein content, improved digestibility, and increasednutraceutical content, e.g., increased phytosterol content, increasedtocopherol content, increased stanol content and/or increased vitamincontent. Polypeptides of interest also include, for example, thoseresulting in or contributing to a reduced content of an unwantedcomponent in a harvested crop, e.g., phytic acid, or sugar degradingenzymes. By “resulting in” or “contributing to” is intended that thepolypeptide of interest can directly or indirectly contribute to theexistence of a trait of interest (e.g., increasing cellulose degradationby the use of a heterologous cellulase enzyme).

In one embodiment, the polypeptide contributes to improved digestibilityfor food or feed. Xylanases are hemicellulolytic enzymes that improvethe breakdown of plant cell walls, which leads to better utilization ofthe plant nutrients by an animal. This leads to improved growth rate andfeed conversion. Also, the viscosity of the feeds containing xylan canbe reduced. Heterologous production of xylanases in plant cells also canfacilitate lignocellulosic conversion to fermentable sugars inindustrial processing.

Numerous xylanases from fungal and bacterial microorganisms have beenidentified and characterized (see, e.g., U.S. Pat. No. 5,437,992;Coughlin et al. (1993) “Proceedings of the Second TRICEL Symposium onTrichoderma reesei Cellulases and Other Hydrolases” Espoo; Souminen andReinikainen, eds. (1993) Foundation for Biotechnical and IndustrialFermentation Research 8:125-135; U.S. Patent Publication No.2005/0208178; and PCT Publication No. WO 03/16654). In particular, threespecific xylanases (XYL-I, XYL-II, and XYL-III) have been identified inT reesei (Tenkanen et al. (1992) Enzyme Microb. Technol. 14:566;Torronen et al. (1992) Bio/Technology 10:1461; and Xu et al. (1998)Appl. Microbiol. Biotechnol. 49:718).

In another embodiment, a polypeptide useful for the invention can be apolysaccharide degrading enzyme. Plants of this invention producing suchan enzyme may be useful for generating, for example, fermentationfeedstocks for bioprocessing. In some embodiments, enzymes useful for afermentation process include alpha amylases, proteases, pullulanases,isoamylases, cellulases, hemicellulases, xylanases, cyclodextringlycotransferases, lipases, phytases, laccases, oxidases, esterases,cutinases, granular starch hydrolyzing enzyme and other glucoamylases.

Polysaccharide-degrading enzymes include: starch degrading enzymes suchas α-amylases (EC 3.2.1.1), glucuronidases (E.C. 3.2.1.131); exo-1,4-α-Dglucanases such as amyloglucosidases and glucoamylase (EC 3.2.1.3),β-amylases (EC 3.2.1.2), α-glucosidases (EC 3.2.1.20), and otherexo-amylases; starch debranching enzymes, such as a) isoamylase (EC3.2.1.68), pullulanase (EC 3.2.1.41), and the like; b) cellulases suchas exo-1,4-3-cellobiohydrolase (EC 3.2.1.91), exo-1,3-β-D-glucanase (EC3.2.1.39), β-glucosidase (EC 3.2.1.21); c) L-arabinases, such asendo-1,5-α-L-arabinase (EC 3.2.1.99), α-arabinosidases (EC 3.2.1.55) andthe like; d) galactanases such as endo-1,4-β-D-galactanase (EC3.2.1.89), endo-1,3-β-D-galactanase (EC 3.2.1.90), α-galactosidase (EC3.2.1.22), β-galactosidase (EC 3.2.1.23) and the like; e) mannanases,such as endo-1,4-β-D-mannanase (EC 3.2.1.78), β-mannosidase (EC3.2.1.25), α-mannosidase (EC 3.2.1.24) and the like; f) xylanases, suchas endo-1,4-β-xylanase (EC 3.2.1.8), β-D-xylosidase (EC 3.2.1.37),1,3-β-D-xylanase, and the like; and g) other enzymes such asα-L-fucosidase (EC 3.2.1.51), α-L-rhamnosidase (EC 3.2.1.40), levanase(EC 3.2.1.65), inulanase (EC 3.2.1.7), and the like. In one embodiment,the α-amylase is the synthetic α-amylase, Amy797E, described is U.S.Pat. No. 8,093,453, herein incorporated by reference in its entirety.

Further enzymes which may be used with the invention include proteases,such as fungal and bacterial proteases. Fungal proteases include, butare not limited to, those obtained from Aspergillus, Trichoderma, Mucorand Rhizopus, such as A. niger, A. awamori, A. oryzae and M. miehei. Insome embodiments, the polypeptides of this invention can becellobiohydrolase (CBH) enzymes (EC 3.2.1.91). In one embodiment, thecellobiohydrolase enzyme can be CBH1 or CBH2.

Other enzymes useful with the invention include, but are not limited to,hemicellulases, such as mannases and arabinofuranosidases (EC 3.2.1.55);ligninases; lipases (e.g., E.C. 3.1.1.3), glucose oxidases, pectinases,xylanases, transglucosidases, alpha 1,6 glucosidases (e.g., E.C.3.2.1.20); esterases such as ferulic acid esterase (EC 3.1.1.73) andacetyl xylan esterases (EC 3.1.1.72); and cutinases (e.g. E.C.3.1.1.74).

In some embodiments, the invention provides a transgenic non-human hostcell comprising a polynucleotide, a nucleic acid molecule, a chimericgene, an expression cassette or a recombinant vector of the invention.The transgenic non-human host cell can include, but is not limited to, aplant cell, a yeast cell, a bacterial cell or an insect cell.Accordingly, in some embodiments, the invention provides a bacterialcell selected from the genera Bacillus, Brevibacillus, Clostridium,Xenorhabdus, Photorhabdus, Pasteuria, Escherichia, Pseudomonas, Erwinia,Serratia, Klebsiella, Salmonella, Pasteurella, Xanthomonas,Streptomyces, Rhizobium, Rhodopseudomonas, Methylophilius,Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter,Leuconostoc, or Alcaligenes. Thus, for example, as biological insectcontrol agents, the Cry proteins of the invention can be produced byexpression of the chimeric gene encoding the Cry proteins of theinvention in a bacterial cell. For example, in one embodiment, aBacillus thuringiensis cell comprising a chimeric gene of the inventionis provided.

In further embodiments, the invention provides a plant cell that is adicot plant cell or a monocot plant cell. In additional embodiments, thedicot plant cell is selected from the group consisting of a soybeancell, sunflower cell, tomato cell, cole crop cell, cotton cell, sugarbeet cell and tobacco cell. In further embodiments, the monocot cell isselected from the group consisting of a barley cell, maize cell, oatcell, rice cell, sorghum cell, sugar cane cell and wheat cell. In someembodiments, the invention provides a plurality of dicot cells ormonocot cells expressing a toxic protein of the invention encoded by achimeric gene of the invention. In other embodiments the plurality ofcells are juxtaposed to form an apoplast and are grown in naturalsunlight.

In another embodiment of the invention, a toxic protein of the inventionis expressed in a higher organism, for example, a plant. In this case,transgenic plants expressing effective amounts of the toxic proteinprotect themselves from plant pests such as insect pests. When theinsect starts feeding on such a transgenic plant, it also ingests theexpressed toxin. This can deter the insect from further biting into theplant tissue or may even harm or kill the insect. A polynucleotide ofthe invention is inserted into an expression cassette, which is thenstably integrated in the genome of the plant. In another embodiment, thepolynucleotide is included in a non-pathogenic self-replicating virus.Plants transformed in accordance with the invention may be monocots ordicots and include, but are not limited to, corn (maize), soybean, rice,wheat, barley, rye, oats, sorghum, millet, sunflower, safflower, sugarbeet, cotton, sugarcane, oilseed rape, alfalfa, tobacco, peanuts,vegetables, including, sweet potato, bean, pea, chicory, lettuce,cabbage, cauliflower, broccoli, turnip, carrot, eggplant, cucumber,radish, spinach, potato, tomato, asparagus, onion, garlic, melons,pepper, celery, squash, pumpkin, zucchini, fruits, including, apple,pear, quince, plum, cherry, peach, nectarine, apricot, strawberry,grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana,and specialty plants, such as Arabidopsis, and woody plants such asconiferous and deciduous trees. Preferably, plants of the of theinvention are crop plants such as maize, sorghum, wheat, sunflower,tomato, crucifers, peppers, potato, cotton, rice, soybean, sugar beet,sugarcane, tobacco, barley, oilseed rape, and the like.

Once a desired polynucleotide has been transformed into a particularplant species, it may be propagated in that species or moved into othervarieties of the same species, particularly including commercialvarieties, using traditional breeding techniques.

A polynucleotide of the invention is expressed in transgenic plants,thus causing the biosynthesis of the corresponding Cry protein in thetransgenic plants. In this way, transgenic plants with enhanced yieldprotection in the presence of insect pressure are generated. For theirexpression in transgenic plants, the nucleotide sequences of theinvention may require modification and optimization. Although in manycases genes from microbial organisms can be expressed in plants at highlevels without modification, low expression in transgenic plants mayresult from microbial nucleotide sequences having codons that are notpreferred in plants. It is known in the art that living organisms havespecific preferences for codon usage, and the codons of the nucleotidesequences described in this invention can be changed to conform withplant preferences, while maintaining the amino acids encoded thereby.Furthermore, high expression in plants, for example corn plants, is bestachieved from coding sequences that have at least about 35% GC content,or at least about 45%, or at least about 50%, or at least about 60%.Microbial nucleotide sequences that have low GC contents may expresspoorly in plants due to the existence of ATTTA motifs that maydestabilize messages, and AATAAA motifs that may cause inappropriatepolyadenylation. Although certain gene sequences may be adequatelyexpressed in both monocotyledonous and dicotyledonous plant species,sequences can be modified to account for the specific codon preferencesand GC content preferences of monocotyledons or dicotyledons as thesepreferences have been shown to differ (Murray et al. Nucl. Acids Res.17:477-498 (1989)). In addition, the nucleotide sequences are screenedfor the existence of illegitimate splice sites that may cause messagetruncation. All changes required to be made within the nucleotidesequences such as those described above are made using well knowntechniques of site directed mutagenesis, PCR, and synthetic geneconstruction using the methods described for example in U.S. Pat. Nos.5,625,136; 5,500,365 and 6,013,523.

In some embodiments, the invention provides synthetic genes madeaccording to the procedure disclosed in U.S. Pat. No. 5,625,136, hereinincorporated by reference. In this procedure, maize preferred codons,i.e., the single codon that most frequently encodes that amino acid inmaize, are used. The maize preferred codon for a particular amino acidcan be derived, for example, from known gene sequences from maize. Forexample, maize codon usage for 28 genes from maize plants is found inMurray et al., Nucleic Acids Research 17:477-498 (1989), the disclosureof which is incorporated herein by reference. Specifically exemplifiedsynthetic sequences of the present invention made with maize optimizedcodons are represented by any one of SEQ ID NOs: 13-20. In this manner,the nucleotide sequences can be optimized for expression in any plant.It is recognized that all or any part of a nucleotide sequence may beoptimized or synthetic. That is, a polynucleotide may comprise anucleotide sequence that is part native sequence and part syntheticoptimized sequence.

For efficient initiation of translation, sequences adjacent to theinitiating methionine may require modification. For example, they can bemodified by the inclusion of sequences known to be effective in plants.Joshi has suggested an appropriate consensus for plants (NAR15:6643-6653 (1987)) and Clonetech suggests a further consensustranslation initiator (1993/1994 catalog, page 210). These consensusesare suitable for use with the nucleotide sequences of this invention.The sequences are incorporated into constructions comprising thenucleotide sequences, up to and including the ATG (while leaving thesecond amino acid unmodified), or alternatively up to and including theGTC subsequent to the ATG (with the possibility of modifying the secondamino acid of the transgene).

The novel cry protein coding sequences of the invention, either as theirnative sequence or as synthetic sequences as described above, can beoperably fused to a variety of promoters for expression in plantsincluding constitutive, inducible, temporally regulated, developmentallyregulated, chemically regulated, tissue-preferred and tissue-specificpromoters to prepare recombinant DNA molecules, i.e., chimeric genes.The choice of promoter will vary depending on the temporal and spatialrequirements for expression, and also depending on the target species.Thus, expression of the nucleotide sequences of this invention inleaves, in stalks or stems, in ears, in inflorescences (e.g. spikes,panicles, cobs, etc.), in roots, and/or seedlings is preferred. In manycases, however, protection against more than one type of insect pest issought, and thus expression in multiple tissues is desirable. Althoughmany promoters from dicotyledons have been shown to be operational inmonocotyledons and vice versa, ideally dicotyledonous promoters areselected for expression in dicotyledons, and monocotyledonous promotersfor expression in monocotyledons. However, there is no restriction tothe provenance of selected promoters; it is sufficient that they areoperational in driving the expression of the nucleotide sequences in thedesired cell.

Examples of constitutive promoters useful in the invention include theCaMV 35S and 19S promoters (Fraley et al., U.S. Pat. No. 5,352,605,incorporated herein by reference). Additionally, a promoter is derivedfrom any one of several of the actin genes, which are expressed in mostcell types. The promoter expression cassettes described by McElroy etal. (Mol. Gen. Genet. 231: 150-160 (1991)) can be easily modified forthe expression of the novel toxin gene and are particularly suitable foruse in monocotyledonous hosts. Yet another constitutive promoter isderived from ubiquitin, which is another gene product known toaccumulate in many cell types. A ubiquitin promoter has been cloned fromseveral species for use in transgenic plants, for example, sunflower(Binet et al., 1991. Plant Science 79: 87-94), maize (Christensen etal., 1989. Plant Molec. Biol. 12: 619-632), and arabidopsis (Norris etal. 1993. Plant Molec. Biol. 21:895-906). The maize ubiquitin promoterhas been developed in transgenic monocot systems and its sequence andvectors constructed for monocot transformation are disclosed in thepatent publication EP 0 342 926. The ubiquitin promoter is suitable forthe expression of the novel toxin gene in transgenic plants, especiallymonocotyledons.

Tissue-specific or tissue-preferential promoters useful for theexpression of the novel cry protein coding sequences of the invention inplants, particularly maize, are those that direct expression in root,pith, leaf or pollen. Such promoters are disclosed in U.S. Pat. No.5,625,136, herein incorporated by reference in its entirety. Othertissue specific promoters useful in the present invention include thecotton rubisco promoter disclosed in U.S. Pat. No. 6,040,504; the ricesucrose synthase promoter disclosed in U.S. Pat. No. 5,604,121; and thecestrum yellow leaf curling virus promoter disclosed in U.S. Pat. No.7,166,770, all incorporated by reference in their entirety. Chemicallyinducible promoters useful for directing the expression of the noveltoxin gene in plants are disclosed in U.S. Pat. No. 5,614,395 hereinincorporated by reference in its entirety.

The nucleotide sequences of this invention can also be expressed underthe regulation of promoters that are chemically regulated. This enablesthe Cry proteins of the invention to be synthesized only when the cropplants are treated with the inducing chemicals. Examples of suchtechnology for chemical induction of gene expression is detailed in thepublished application EP 0 332 104 and U.S. Pat. No. 5,614,395. In oneembodiment, the chemically regulated promoter is the tobacco PR-1apromoter.

Another category of promoters useful in the invention is that which iswound inducible. Numerous promoters have been described which areexpressed at wound sites and also at the sites of phytopathogeninfection. Ideally, such a promoter should only be active locally at thesites of insect invasion, and in this way the insecticidal proteins onlyaccumulate in cells that need to synthesize the insecticidal proteins tokill the invading insect pest. Examples of promoters of this kindinclude those described by Stanford et al. Mol. Gen. Genet. 215:200-208(1989), Xu et al. Plant Molec. Biol. 22:573-588 (1993), Logemann et al.Plant Cell 1:151-158 (1989), Rohrmeier & Lehle, Plant Molec. Biol.22:783-792 (1993), Firek et al. Plant Molec. Biol. 22:129-142 (1993),and Warner et al. Plant J. 3:191-201 (1993).

Non-limiting examples of promoters that cause tissue specific expressionpatterns that are useful in the invention include green tissue specific,root specific, stem specific, and/or flower specific. Promoters suitablefor expression in green tissue include many that regulate genes involvedin photosynthesis and many of these have been cloned from bothmonocotyledons and dicotyledons. One such promoter is the maize PEPCpromoter from the phosphoenol carboxylase gene (Hudspeth & Grula, PlantMolec. Biol. 12:579-589 (1989)). Another promoter for root specificexpression is that described by de Framond (FEBS 290:103-106 (1991) orU.S. Pat. No. 5,466,785). Another promoter useful in the invention isthe stem specific promoter described in U.S. Pat. No. 5,625,136, whichnaturally drives expression of a maize trpA gene.

In addition to the selection of a suitable promoter, constructs forexpression of an insecticidal toxin in plants require an appropriatetranscription terminator to be operably linked downstream of theheterologous nucleotide sequence. Several such terminators are availableand known in the art (e.g. tm1 from CaMV, E9 from rbcS). Any availableterminator known to function in plants can be used in the context ofthis invention.

Numerous other sequences can be incorporated into expression cassettesdescribed in this invention. These include sequences that have beenshown to enhance expression such as intron sequences (e.g. from Adh1 andbronzel) and viral leader sequences (e.g. from TMV, MCMV and AMV).

It may be preferable to target expression of the nucleotide sequences ofthe present invention to different cellular localizations in the plant.In some cases, localization in the cytosol may be desirable, whereas inother cases, localization in some subcellular organelle may bepreferred. Any mechanism for targeting gene products, e.g., in plants,can be used to practice this invention, and such mechanisms are known toexist in plants and the sequences controlling the functioning of thesemechanisms have been characterized in some detail. Sequences have beencharacterized which cause the targeting of gene products to other cellcompartments Amino terminal sequences can be responsible for targeting aprotein of interest to any cell compartment, such as, a vacuole,mitochondrion, peroxisome, protein bodies, endoplasmic reticulum,chloroplast, starch granule, amyloplast, apoplast or cell wall of aplant (e.g. Unger et. al. Plant Molec. Biol. 13: 411-418 (1989); Rogerset. al. (1985) Proc. Natl. Acad. Sci. USA 82: 6512-651; U.S. Pat. No.7,102,057; WO 2005/096704, all of which are hereby incorporated byreference. Optionally, the signal sequence may be an N-terminal signalsequence from waxy, an N-terminal signal sequence from gamma-zein, astarch binding domain, a C-terminal starch binding domain, a chloroplasttargeting sequence, which imports the mature protein to the chloroplast(Comai et. al. (1988) J. Biol. Chem. 263: 15104-15109; van den Broeck,et. al. (1985) Nature 313: 358-363; U.S. Pat. No. 5,639,949) or asecretion signal sequence from aleurone cells (Koehler & Ho, Plant Cell2: 769-783 (1990)). Additionally, amino terminal sequences inconjunction with carboxy terminal sequences are responsible for vacuolartargeting of gene products (Shinshi et. al. (1990) Plant Molec. Biol.14: 357-368). In one embodiment, the signal sequence selected includesthe known cleavage site, and the fusion constructed takes into accountany amino acids after the cleavage site(s), which are required forcleavage. In some cases this requirement may be fulfilled by theaddition of a small number of amino acids between the cleavage site andthe transgene ATG or, alternatively, replacement of some amino acidswithin the transgene sequence. These construction techniques are wellknown in the art and are equally applicable to any cellular compartment.

It will be recognized that the above-described mechanisms for cellulartargeting can be utilized not only in conjunction with their cognatepromoters, but also in conjunction with heterologous promoters so as toeffect a specific cell-targeting goal under the transcriptionalregulation of a promoter that has an expression pattern different tothat of the promoter from which the targeting signal derives.

Plant Transformation

Procedures for transforming plants are well known and routine in the artand are described throughout the literature. Non-limiting examples ofmethods for transformation of plants include transformation viabacterial-mediated nucleic acid delivery (e.g., via Agrobacterium),viral-mediated nucleic acid delivery, silicon carbide or nucleic acidwhisker-mediated nucleic acid delivery, liposome mediated nucleic aciddelivery, microinjection, microparticle bombardment,calcium-phosphate-mediated transformation, cyclodextrin-mediatedtransformation, electroporation, nanoparticle-mediated transformation,sonication, infiltration, PEG-mediated nucleic acid uptake, as well asany other electrical, chemical, physical (mechanical) and/or biologicalmechanism that results in the introduction of nucleic acid into theplant cell, including any combination thereof General guides to variousplant transformation methods known in the art include Miki et al.(“Procedures for Introducing Foreign DNA into Plants” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E., Eds. (CRC Press, Inc., Boca Raton, 1993), pages 67-88) andRakowoczy-Trojanowska (Cell. Mol. Biol. Lett. 7:849-858 (2002)).

For Agrobacterium-mediated transformation, binary vectors or vectorscarrying at least one T-DNA border sequence are suitable, whereas fordirect gene transfer (e.g., particle bombardment and the like) anyvector is suitable and linear DNA containing only the construction ofinterest can be used. In the case of direct gene transfer,transformation with a single DNA species or co-transformation can beused (Schocher et al., Biotechnology 4:1093-1096 (1986)). For bothdirect gene transfer and Agrobacterium-mediated transfer, transformationis usually (but not necessarily) undertaken with a selectable markerthat may be a positive selection (Phosphomannose Isomerase), provideresistance to an antibiotic (kanamycin, hygromycin or methotrexate) or aherbicide (glyphosate or glufosinate). However, the choice of selectablemarker is not critical to the invention.

Agrobacterium-mediated transformation is a commonly used method fortransforming plants, in particular, dicot plants, because of its highefficiency of transformation and because of its broad utility with manydifferent species. Agrobacterium-mediated transformation typicallyinvolves transfer of the binary vector carrying the foreign DNA ofinterest to an appropriate Agrobacterium strain that may depend on thecomplement of vir genes carried by the host Agrobacterium strain eitheron a co-resident Ti plasmid or chromosomally (Uknes et al. (1993) PlantCell 5:159-169). The transfer of the recombinant binary vector toAgrobacterium can be accomplished by a triparental mating procedureusing Escherichia coli carrying the recombinant binary vector, a helperE. coli strain that carries a plasmid that is able to mobilize therecombinant binary vector to the target Agrobacterium strain.Alternatively, the recombinant binary vector can be transferred toAgrobacterium by nucleic acid transformation (Höfgen & Willmitzer (1988)Nucleic Acids Res. 16:9877).

Transformation of a plant by recombinant Agrobacterium usually involvesco cultivation of the Agrobacterium with explants from the plant andfollows methods well known in the art. Transformed tissue is regeneratedon selection medium carrying an antibiotic or herbicide resistancemarker between the binary plasmid T-DNA borders.

As discussed previously, another method for transforming plants, plantparts and plant cells involves propelling inert or biologically activeparticles at plant tissues and cells. See, e.g., U.S. Pat. Nos.4,945,050; 5,036,006 and 5,100,792. Generally, this method involvespropelling inert or biologically active particles at the plant cellsunder conditions effective to penetrate the outer surface of the celland afford incorporation within the interior thereof. When inertparticles are utilized, the vector can be introduced into the cell bycoating the particles with the vector containing the nucleic acid ofinterest. Alternatively, a cell or cells can be surrounded by the vectorso that the vector is carried into the cell by the wake of the particle.Biologically active particles (e.g., a dried yeast cell, a driedbacterium or a bacteriophage, each containing one or more nucleic acidssought to be introduced) also can be propelled into plant tissue.

In another embodiment, a polynucleotide of the invention can be directlytransformed into the plastid genome. A major advantage of plastidtransformation is that plastids are generally capable of expressingbacterial genes without substantial modification, and plastids arecapable of expressing multiple open reading frames under control of asingle promoter. Plastid transformation technology is extensivelydescribed in U.S. Pat. Nos. 5,451,513, 5,545,817, and 5,545,818, in PCTapplication no. WO 95/16783, and in McBride et al. (1994) Proc. Natl.Acad. Sci. USA 91, 7301-7305. The basic technique for chloroplasttransformation involves introducing regions of cloned plastid DNAflanking a selectable marker together with the gene of interest into asuitable target tissue, e.g., using biolistics or protoplasttransformation (e.g., calcium chloride or PEG mediated transformation).The 1 to 1.5 kb flanking regions, termed targeting sequences, facilitatehomologous recombination with the plastid genome and thus allow thereplacement or modification of specific regions of the plastome.Initially, point mutations in the chloroplast 16S rRNA and rps12 genesconferring resistance to spectinomycin and/or streptomycin can beutilized as selectable markers for transformation (Svab, Z.,Hajdukiewicz, P., and Maliga, P. (1990) Proc. Natl. Acad. Sci. USA 87,8526-8530; Staub, J. M., and Maliga, P. (1992) Plant Cell 4, 39-45). Thepresence of cloning sites between these markers allows creation of aplastid targeting vector for introduction of foreign genes (Staub, J.M., and Maliga, P. (1993) EMBO J. 12, 601-606). Substantial increases intransformation frequency can be obtained by replacement of the recessiverRNA or r-protein antibiotic resistance genes with a dominant selectablemarker, the bacterial aadA gene encoding the spectinomycin-cletoxifyingenzyme aminoglycoside-3′-adenyltransferase (Svab, Z., and Maliga, P.(1993) Proc. Natl. Acad. Sci. USA 90, 913-917). Previously, this markerhad been used successfully for high-frequency transformation of theplastid genome of the green alga Chlamydomonas reinhardtii(Goldschmidt-Clermont, M. (1991) Nucl. Acids Res. 19:4083-4089). Otherselectable markers useful for plastid transformation are known in theart and encompassed within the scope of the invention. Typically,approximately 15-20 cell division cycles following transformation arerequired to reach a homoplastidic state. Plastid expression, in whichgenes are inserted by homologous recombination into all of the severalthousand copies of the circular plastid genome present in each plantcell, takes advantage of the enormous copy number advantage overnuclear-expressed genes to permit expression levels that can readilyexceed 10% of the total soluble plant protein. In one embodiment, apolynucleotide of the invention can be inserted into a plastid-targetingvector and transformed into the plastid genome of a desired plant host.Thus, plants homoplastic for plastid genomes containing a nucleotidesequence of the invention can be obtained, which are capable of highexpression of the polynucleotide.

Methods of selecting for transformed, transgenic plants, plant cellsand/or plant tissue culture are routine in the art and can be employedin the methods of the invention provided herein. For example, arecombinant vector of the invention also can include an expressioncassette comprising a nucleotide sequence for a selectable marker, whichcan be used to select a transformed plant, plant part and/or plant cell.As used herein, “selectable marker” means a nucleotide sequence thatwhen expressed imparts a distinct phenotype to the plant, plant partand/or plant cell expressing the marker and thus allows such transformedplants, plant parts and/or plant cells to be distinguished from thosethat do not have the marker. Such a nucleotide sequence may encodeeither a selectable or screenable marker, depending on whether themarker confers a trait that can be selected for by chemical means, suchas by using a selective agent (e.g., an antibiotic, herbicide, or thelike), or on whether the marker is simply a trait that one can identifythrough observation or testing, such as by screening (e.g., the R-locustrait). Of course, many examples of suitable selectable markers areknown in the art and can be used in the expression cassettes describedherein.

Examples of selectable markers include, but are not limited to, anucleotide sequence encoding neo or nptII, which confers resistance tokanamycin, G418, and the like (Potrykus et al. (1985) Mol. Gen. Genet.199:183-188); a nucleotide sequence encoding bar, which confersresistance to phosphinothricin; a nucleotide sequence encoding analtered 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, whichconfers resistance to glyphosate (Hinchee et al. (1988) Biotech.6:915-922); a nucleotide sequence encoding a nitrilase such as bxn fromKlebsiella ozaenae that confers resistance to bromoxynil (Stalker et al.(1988) Science 242:419-423); a nucleotide sequence encoding an alteredacetolactate synthase (ALS) that confers resistance to imidazolinone,sulfonylurea or other ALS-inhibiting chemicals (EP Patent ApplicationNo. 154204); a nucleotide sequence encoding a methotrexate-resistantdihydrofolate reductase (DHFR) (Thillet et al. (1988) J. Biol. Chem.263:12500-12508); a nucleotide sequence encoding a dalapon dehalogenasethat confers resistance to dalapon; a nucleotide sequence encoding amannose-6-phosphate isomerase (also referred to as phosphomannoseisomerase (PMI)) that confers an ability to metabolize mannose (U.S.Pat. Nos. 5,767,378 and 5,994,629); a nucleotide sequence encoding analtered anthranilate synthase that confers resistance to 5-methyltryptophan; and/or a nucleotide sequence encoding hph that confersresistance to hygromycin. One of skill in the art is capable of choosinga suitable selectable marker for use in an expression cassette of thisinvention.

Additional selectable markers include, but are not limited to, anucleotide sequence encoding β-glucuronidase or uidA (GUS) that encodesan enzyme for which various chromogenic substrates are known; an R-locusnucleotide sequence that encodes a product that regulates the productionof anthocyanin pigments (red color) in plant tissues (Dellaporta et al.,“Molecular cloning of the maize R-nj allele by transposon-tagging withAc” 263-282 In: Chromosome Structure and Function: Impact of NewConcepts, 18th Stadler Genetics Symposium (Gustafson & Appels eds.,Plenum Press 1988)); a nucleotide sequence encoding β-lactamase, anenzyme for which various chromogenic substrates are known (e.g., PADAC,a chromogenic cephalosporin) (Sutcliffe (1978) Proc. Natl. Acad. Sci.USA 75:3737-3741); a nucleotide sequence encoding xylE that encodes acatechol dioxygenase (Zukowsky et al. (1983) Proc. Natl. Acad. Sci. USA80:1101-1105); a nucleotide sequence encoding tyrosinase, an enzymecapable of oxidizing tyrosine to DOPA and dopaquinone, which in turncondenses to form melanin (Katz et al. (1983) J. Gen. Microbiol.129:2703-2714); a nucleotide sequence encoding β-galactosidase, anenzyme for which there are chromogenic substrates; a nucleotide sequenceencoding luciferase (lux) that allows for bioluminescence detection (Owet al. (1986) Science 234:856-859); a nucleotide sequence encodingaequorin which may be employed in calcium-sensitive bioluminescencedetection (Prasher et al. (1985) Biochem. Biophys. Res. Comm.126:1259-1268); or a nucleotide sequence encoding green fluorescentprotein (Niedz et al. (1995) Plant Cell Reports 14:403-406). One ofskill in the art is capable of choosing a suitable selectable marker foruse in an expression cassette of this invention.

Further, as is well known in the art, intact transgenic plants can beregenerated from transformed plant cells, plant tissue culture and/orcultured protoplasts using any of a variety of known techniques. Plantregeneration from plant cells, plant tissue culture and/or culturedprotoplasts is described, for example, in Evans et al. (Handbook ofPlant Cell Cultures, Vol. 1, MacMilan Publishing Co. New York (1983));and Vasil I. R. (ed.) (Cell Culture and Somatic Cell Genetics of Plants,Acad. Press, Orlando, Vol. I (1984), and Vol. II (1986)).

Additionally, the genetic properties engineered into the transgenicseeds and plants, plant parts, and/or plant cells of the inventiondescribed above can be passed on by sexual reproduction or vegetativegrowth and therefore can be maintained and propagated in progeny plants.Generally, maintenance and propagation make use of known agriculturalmethods developed to fit specific purposes such as harvesting, sowing ortilling.

A polynucleotide therefore can be introduced into the plant, plant partand/or plant cell in any number of ways that are well known in the art,as described above. Therefore, no particular method for introducing oneor more polynucleotides into a plant is relied upon, rather any methodthat allows the one or more polynucleotides to be stably integrated intothe genome of the plant can be used. Where more than one polynucleotidesis to be introduced, the respective polynucleotides can be assembled aspart of a single nucleic acid molecule, or as separate nucleic acidmolecules, and can be located on the same or different nucleic acidmolecules. Accordingly, the polynucleotides can be introduced into thecell of interest in a single transformation event, in separatetransformation events, or, for example, in plants, as part of a breedingprotocol.

Additional embodiments of the invention include harvested productsproduced from the transgenic plants and/or parts thereof of theinvention, as well as a processed product produced from the harvestedproducts. A harvested product can be a whole plant or any plant part, asdescribed herein. Thus, in some embodiments, non-limiting examples of aharvested product include a seed, a fruit, a flower or part thereof(e.g., an anther, a stigma, and the like), a leaf, a stem, and the like.In other embodiments, a processed product includes, but is not limitedto, a flour, meal, oil, starch, cereal, and the like produced from aharvested seed or other plant part of the invention, wherein said seedor other plant part comprises a nucleic acidmolecule/polynucleotide/nucleotide sequence of this invention.

In other embodiments, the invention provides an extract from atransgenic seed and/or a transgenic plant of the invention, wherein theextract comprises a nucleic acid molecule, a polynucleotide, anucleotide sequence or a toxic protein of the invention. Extracts fromplants or plant parts can be made according to procedures well known inthe art (See, de la Tone et al., Food, Agric. Environ. 2(1):84-89(2004); Guidet, Nucleic Acids Res. 22(9): 1772-1773 (1994); Lipton etal., Food Agric. Immun. 12:153-164 (2000)).

Insecticidal Compositions

In some embodiments, the invention provides an insecticidal compositioncomprising a Cry protein of the invention in an agriculturallyacceptable carrier. As used herein an “agriculturally-acceptablecarrier” can include natural or synthetic, organic or inorganic materialwhich is combined with the active component to facilitate itsapplication to the plant, or part thereof. Examples of agriculturallyacceptable carriers include, without limitation, powders, dusts,pellets, granules, sprays, emulsions, colloids, and solutions.Agriculturally-acceptable carriers further include, but are not limitedto, inert components, dispersants, surfactants, adjuvants, tackifiers,stickers, binders, or combinations thereof, that can be used inagricultural formulations. Such compositions can be applied in anymanner that brings the pesticidal proteins or other pest control agentsin contact with the pests. Accordingly, the compositions can be appliedto the surfaces of plants or plant parts, including seeds, leaves,flowers, stems, tubers, roots, and the like. Another agriculturallyacceptable carrier may be a transgenic plant or plant part.

In further embodiments, the insecticidal composition comprises atransgenic bacterial cell of the invention, wherein the bacterial cellcomprises a chimeric gene of the invention. For example, such aninsecticidal composition can be prepared by desiccation, lyophilization,homogenization, extraction, filtration, centrifugation, sedimentation,or concentration of a culture of Bacillus thuringiensis cells comprisinga polynucleotide of the invention. In additional embodiments, thecomposition comprises from about 1% to about 99% by weight of the Cryprotein of the invention.

The Cry proteins of the invention can be used in combination with otherpest control agents to increase pest target range or for the preventionand/or management of insect resistance. Therefore, in some embodiments,the invention provides a composition that controls one or more plantpests, wherein the composition comprises a first Cry protein of theinvention and a second pest control agent different from the first Cryprotein. In other embodiments, the composition is a formulation fortopical application to a plant. In still other embodiments, thecomposition is a transgenic plant. In further embodiments, thecomposition is a combination of a formulation topically applied to atransgenic plant. In one embodiment, the formulation comprises the firstCry protein of the invention when the transgenic plant comprises thesecond pest control agent. In another embodiment, the formulationcomprises the second pest control agent when the transgenic plantcomprises the first Cry protein of the invention.

In some embodiments, the second pest control agent can be an agentselected from the group consisting of a chemical pesticide, a Bacillusthuringiensis (Bt) insecticidal protein, a Xenorhabdus insecticidalprotein, a Photorhabdus insecticidal protein, a Brevibacilluslaterosporus insecticidal protein, a Bacillus sphaericus insecticidalprotein, a protease inhibitors (both serine and cysteine types),lectins, alpha-amylase, peroxidase and cholesterol oxidase.

In other embodiments, the second pest control agent is a chemicalpesticide selected from the group consisting of pyrethroids, carbamates,neonicotinoids, neuronal sodium channel blockers, insecticidalmacrocyclic lactones, .gamma.-aminobutyric acid (GABA) antagonists,insecticidal ureas and juvenile hormone mimics. In another embodiment,the chemical pesticide is selected from the group consisting ofabamectin, acephate, acetamiprid, amidoflumet (S-1955), avermectin,azadirachtin, azinphos-methyl, bifenthrin, binfenazate, buprofezin,carbofuran, chlorfenapyr, chlorfluazuron, chlorpyrifos,chlorpyrifos-methyl, chromafenozide, clothianidin, cyfluthrin,beta-cyfluthrin, cyhalothrin, lambda-cyhalothrin, cypermethrin,cyromazine, deltamethrin, diafenthiuron, diazinon, diflubenzuron,dimethoate, diofenolan, emamectin, endosulfan, esfenvalerate, ethiprole,fenothicarb, fenoxycarb, fenpropathrin, fenproximate, fenvalerate,fipronil, flonicamid, flucythrinate, tau-fluvalinate, flufenerim(UR-50701), flufenoxuron, fonophos, halofenozide, hexaflumuron,imidacloprid, indoxacarb, isofenphos, lufenuron, malathion, metaldehyde,methamidophos, methidathion, methomyl, methoprene, methoxychlor,monocrotophos, methoxyfenozide, nithiazin, novaluron, noviflumuron(XDE-007), oxamyl, parathion, parathion-methyl, permethrin, phorate,phosalone, phosmet, phosphamidon, pirimicarb, profenofos, pymetrozine,pyridalyl, pyriproxyfen, rotenone, spinosad, spiromesifin (BSN 2060),sulprofos, tebufenozide, teflubenzuron, tefluthrin, terbufos,tetrachlorvinphos, thiacloprid, thiamethoxam, thiodicarb,thiosultap-sodium, tralomethrin, trichlorfon and triflumuron, aldicarb,oxamyl, fenamiphos, amitraz, chinomethionat, chlorobenzilate, cyhexatin,dicofol, dienochior, etoxazole, fenazaquin, fenbutatin oxide,fenpropathrin, fenpyroximate, hexythiazox, propargite, pyridaben andtebufenpyrad. In another embodiment, the chemical pesticide is selectedfrom the group consisting of cypermethrin, cyhalothrin, cyfluthrin andbeta-cyfluthrin, esfenvalerate, fenvalerate, tralomethrin, fenothicarb,methomyl, oxamyl, thiodicarb, clothianidin, imidacloprid, thiacloprid,indoxacarb, spinosad, abamectin, avermectin, emamectin, endosulfan,ethiprole, fipronil, flufenoxuron, triflumuron, diofenolan,pyriproxyfen, pymetrozine and amitraz.

In additional embodiments, the second pest control agent can be one ormore of any number of Bacillus thuringiensis insecticidal proteinsincluding but not limited to a Cry protein, a vegetative insecticidalprotein (VIP) and insecticidal chimeras of any of the precedinginsecticidal proteins. In other embodiments, the second pest controlagent is a Cry protein selected from the group consisting of Cry1Aa,Cry1Ab, Cry1Ac, Cry1Ad, Cry1Ae, Cry1Af, Cry1Ag, Cry1Ah, Cry1Ai, Cry1Aj,Cry1Ba, Cry1Bb, Cry1Bc, Cry1Bd, Cry1Be, Cry1Bf, Cry1Bg, Cry1Bh, Cry1Bi,Cry1Aa, Cry1Cb, Cry1Da, Cry1Db, Cry1Dc, Cry1Dd, Cry1Ea, Cry1Eb, Cry1Fa,Cry1Fb, Cry1Ga, Cry1Gb, Cry1Gc, Cry1Ha, Cry1Hb, Cry1Hc, Cry1Ia, Cry1Ib,Cry1Ic, Cry1Id, Cry1Ie, Cry1If, Cry1Ig, Cry1Ja, Cry1Jb, Cry1Jc, Cry1Jd,Cry1Ka, Cry1La, Cry1Ma, Cry1Na, Cry1Nb, Cry2Aa, Cry2Ab, Cry2Ac, Cry2Ad,Cry2Ae, Cry2Af, Cry2Ag, Cry2Ah, Cry2Ai, Cry2Aj, Cry2Ak,Cry2A1, Cry2Ba,Cry3Aa, Cry3Ba, Cry3Bb, Cry3Ca, Cry4Aa, Cry4Ba, Cry4Ca, Cry4Cb, Cry4Cc,Cry5Aa, Cry5Ab, Cry5Ac, Cry5Ad, Cry5Ba, Cry5Ca, Cry5Da, Cry5Ea, Cry6Aa,Cry6Ba, Cry7Aa, Cry7Ab, Cry7Ac, Cry7Ba, Cry7Bb, Cry7Ca, Cry7Cb, Cry7Da,Cry7Ea, Cry7Fa, Cry7Fb, Cry7Ga, Cry7Gb, Cry7Gc, Cry7Gd, Cry7Ha, Cry7Ia,Cry7Ja, Cry7Ka, Cry7Kb, Cry7La, Cry8Aa, Cry8Ab, Cry8Ac, Cry8Ad, Cry8Ba,Cry8Bb, Cry8Bc, Cry8Ca, Cry8Da, Cry8Db, Cry8Ea, Cry8Fa, Cry8Ga, Cry8Ha,Cry8la, Cry8Ib, Cry8Ja, Cry8Ka, Cry8Kb, Cry8La, Cry8Ma, Cry8Na, Cry8Pa,Cry8Qa, Cry8Ra, Cry8Sa, Cry8Ta, Cry9Aa, Cry9Ba, Cry9Bb, Cry9Ca, Cry9Da,Cry9Db, Cry9Dc, Cry9Ea, Cry9Eb, Cry9Ec, Cry9Ed, Cry9Ee, Cry9Fa, Cry9Ga,Cry10Aa, Cry11Aa, Cry11Ba, Cry11Bb, Cry12Aa,Cry13Aa, Cry14Aa, Cry14Ab,Cry15Aa, Cry16Aa, Cry17Aa, Cry18Aa, Cry18Ba, Cry18Ca, Cry19Aa, Cry19Ba,Cry19Ca, Cry20Aa, Cry20Ba, Cry21Aa, Cry21ba, Cry21Ca, Cry21Da, Cry21Ea,Cry21Fa, Cry21Ga, Cry21Ha, Cry22Aa, Cry22Ab, Cry22Ba, Cry22Bb, Cry23Aa,Cry24Aa, Cry24Ba, Cry24Ca, Cry25Aa, Cry26Aa, Cry27Aa, Cry28Aa, Cry29Aa,Cry29Ba, Cry30Aa, Cry30Ba, Cry30Ca, Cry30Da, Cry30Db, Cry30Ea, Cry30Fa,Cry30Ga, Cry31Aa, Cry31Ab, Cry31Ac, Cry31Ad, Cry32Aa, Cry32Ab, Cry32Ba,Cry32Ca, Cry32Cb, Cry32Da, Cry32Ea, Cry32Eb, Cry32Fa, Cry32Ga, Cry32Ha,Cry32Hb, Cry32Ia, Cry32Ja, Cry32Ka, Cry32La, Cry32Ma, Cry32Mb, Cry32Na,Cry32Ga, Cry32Pa, Cry32Qa, Cry32Ra, Cry32Sa, Cry32Ta, Cry32Ua, Cry33Aa,Cry34Aa, Cry34Ab, Cry34Ac, Cry34Ba, Cry35Aa, Cry35Ab, Cry35Ac, Cry35Ba,Cry36Aa, Cry37Aa, Cry38Aa, Cry39Aa, Cry40Aa, Cry40Ba, Cry40Ca, Cry40Da,Cry41Aa, Cry41Ab, Cry41Ba, Cry42Aa, Cry43Aa, Cry43Ba, Cry43Ca, Cry43Cb,Cry43Cc, Cry44Aa, Cry45Aa, Cry46Aa Cry46Ab, Cry47Aa, Cry48Aa, Cry48Ab,Cry49Aa, Cry49Ab, Cry50Aa, Cry50Ba, Cry51Aa, Cry52Aa, Cry52Ba, Cry53Aa,Cry53Ab, Cry54Aa, Cry54Ab, Cry54Ba, Cry55Aa, Cry56Aa, Cry57Aa, Cry57Ab,Cry58Aa, Cry59Aa, Cry59Ba, Cry60Aa, Cry60Ba, Cry61Aa, Cry62Aa, Cry63Aa,Cry64Aa, Cry65Aa, Cry66Aa, Cry67Aa, Cry68Aa, Cry69Aa, Cry69Ab, Cry70Aa,Cry70Ba, Cry70Bb, Cry71Aa, Cry72Aa and Cry73Aa.

In further embodiments, the second pest control agent is a Vip3vegetative insecticidal protein selected from the group consisting ofVip3Aa1, Vip3Aa2, Vip3Aa3, Vip3Aa4, Vip3Aa5, Vip3Aa6, Vip3Aa7, Vip3Aa8,Vip3Aa9, Vip3Aa10, Vip3Aa11, Vip3Aa12, Vip3Aa13, Vip3Aa14, Vip3Aa15,Vip3Aa16, Vip3Aa17, Vip3Aa18, Vip3Aa19, Vip3Aa20, Vip3Aa21, Vip3Aa22,Vip3Aa2, Vip3Aa24, Vip3Aa25, Vip3Aa26, Vip3Aa27, Vip3Aa28, Vip3Aa29,Vip3Aa30, Vip3Aa31, Vip3Aa32, Vip3Aa33, Vip3Aa34, Vip3Aa35, Vip3Aa36,Vip3Aa37, Vip3Aa38, Vip3Aa39, Vip3Aa40, Vip3Aa41, Vip3Aa42, Vip3Aa43,Vip3Aa44, Vip3Ab1, Vip3Ab2, Vip3Ac1, Vip3Ad1, Vip3Ad2, Vip3Ae1, Vip3Af1,Vip3Af2, Vip3Af3, Vip3Ag1, Vip3Ag2,Vip3Ag3 HM117633, Vip3Ag4, Vip3Ag5,Vip3Ah1, Vip3Ba1, Vip3Ba2, Vip3Bb1, Vip3Bb2 and Vip3Bb3.

In still further embodiments, the first Cry protein of the invention andthe second pest control agent are co-expressed in a transgenic plant.This co-expression of more than one pesticidal principle in the sametransgenic plant can be achieved by genetically engineering a plant tocontain and express all the genes necessary. Alternatively, a plant,Parent 1, can be genetically engineered for the expression of the Cryprotein of the invention. A second plant, Parent 2, can be geneticallyengineered for the expression of the second pest control agent. Bycrossing Parent 1 with Parent 2, progeny plants are obtained whichexpress all the genes introduced into Parents 1 and 2.

In additional embodiments, a method of producing a protein toxic to atleast European corn borer (Ostrinia nubilalis) is provided, the methodcomprising: culturing a transgenic non-human host cell that comprisespolynucleotide or a chimeric gene or nucleic acid molecule or arecombinant vector of the invention under conditions in which the hostproduces a protein toxic to at least European corn borer (Ostrinianubilalis). In some embodiments, the transgenic non-human host cell is aplant cell. In one embodiment, the plant cell is a maize cell. In otherembodiments, the conditions under which the plant cell or maize cell aregrown include natural sunlight. In other embodiments, the transgenicnon-human host cell is a bacterial cell. In still other embodiments, thetransgenic non-human host cell is a yeast cell.

In other embodiments, the produced protein has insecticidal activityagainst at least one additional insect, wherein the additional insect isselected from the group consisting of black cutworm (Agrotis ipsilon),fall armyworm (Spodoptera frugiperda), corn earworm (Helicoverpa zea),sugarcane borer (Diatraea saccharalis), velvetbean caterpillar(Anticarsia gemmatalis), soybean looper (Chrysodeixis includes),southwest corn borer (Diatraea grandiosella), western bean cutworm(Richia albicosta), tobacco budworm (Heliothis virescens), Asian cornborer (Ostrinia furnacalis), cotton bollworm (Helicoverpa armigera),striped stem borer (Chilo suppressalis), pink stem borer (Sesamiacalamistis) or rice leaffolder (Cnaphalocrocis medinalis), and anycombination thereof.

In other embodiments, the chimeric gene comprises any of SEQ ID NOs:1-5.In still other embodiments, the produced protein comprises an amino acidsequence of any of SEQ ID NOs: 16-20.

In some embodiments, the chimeric gene comprises a nucleotide sequencethat is codon optimized for expression in a plant. In other embodiments,the chimeric gene comprises any of SEQ ID NOs:6-15. In furtherembodiments, the produced protein comprises an amino acid sequence ofany of SEQ ID NOs:16-25.

In further embodiments, the invention provides a method of producing apest-resistant (e.g., an insect-resistant) transgenic plant, comprising:introducing into a plant a polynucleotide, a chimeric gene, arecombinant vector, an expression cassette or a nucleic acid molecule ofthe invention comprising a nucleotide sequence that encodes a Cryprotein of the invention, wherein the nucleotide sequence is expressedin the plant, thereby conferring to the plant resistance to at leastEuropean corn borer, and producing a pest-resistant (e.g., aninsect-resistant) transgenic plant. In some embodiments, apest-resistant transgenic plant is resistant to at least black cutworm(Agrotis ipsilon) as compared to a control plant lacking thepolynucleotide, chimeric gene, recombinant vector, expression cassetteor nucleic acid molecule of the invention. In some embodiments, theintroducing is achieved by transforming the plant. In other embodiments,the introducing is achieved by crossing a first plant comprising thechimeric gene, recombinant vector, expression cassette or nucleic acidmolecule of the invention with a different second plant.

In some embodiments, a transgenic plant of the invention that isresistant to at least European corn borer (Ostrinia nubilalis) isfurther resistant to at one additional insect, wherein the additionalinsect includes, but is not limited to, black cutworm (Agrotis ipsilon),fall armyworm (Spodoptera frugiperda), corn earworm (Helicoverpa zea),sugarcane borer (Diatraea saccharalis), velvetbean caterpillar(Anticarsia gemmatalis), soybean looper (Chrysodeixis includes),southwest corn borer (Diatraea grandiosella), western bean cutworm(Richia albicosta), tobacco budworm (Heliothis virescens), Asian cornborer (Ostrinia furnacalis), cotton bollworm (Helicoverpa armigera),striped stem borer (Chilo suppressalis), pink stem borer (Sesamiacalamistis) or rice leaffolder (Cnaphalocrocis medinalis), and anycombination thereof.

In further embodiments, a method of controlling at least black cutworm(Agrotis ipsilon) insects is provided, the method comprising deliveringto the insects an effective amount of a Cry protein of the invention. Tobe effective, the Cry protein is first orally ingested by the insect.However, the Cry protein can be delivered to the insect in manyrecognized ways. The ways to deliver a protein orally to an insectinclude, but are not limited to, providing the protein (1) in atransgenic plant, wherein the insect eats (ingests) one or more parts ofthe transgenic plant, thereby ingesting the polypeptide that isexpressed in the transgenic plant; (2) in a formulated proteincomposition(s) that can be applied to or incorporated into, for example,insect growth media; (3) in a protein composition(s) that can be appliedto the surface, for example, sprayed, onto the surface of a plant part,which is then ingested by the insect as the insect eats one or more ofthe sprayed plant parts; (4) a bait matrix; (5) via injection into theinsect; or (6) any other art-recognized protein delivery system. Thus,any method of oral delivery to an insect can be used to deliver thetoxic Cry proteins of the invention. In some particular embodiments, theCry protein of the invention is delivered orally to an insect, whereinthe insect ingests one or more parts of a transgenic plant.

In other embodiments, the Cry protein of the invention is deliveredorally to an insect, wherein the insect ingests one or more parts of aplant sprayed with a composition comprising the Cry proteins of theinvention. Delivering the compositions of the invention to a plantsurface can be done using any method known to those of skill in the artfor applying compounds, compositions, formulations and the like to plantsurfaces. Some non-limiting examples of delivering to or contacting aplant or part thereof include spraying, dusting, sprinkling, scattering,misting, atomizing, broadcasting, soaking, soil injection, soilincorporation, drenching (e.g., root, soil treatment), dipping, pouring,coating, leaf or stem infiltration, side dressing or seed treatment, andthe like, and combinations thereof. These and other procedures forcontacting a plant or part thereof with compound(s), composition(s) orformulation(s) are well-known to those of skill in the art.

In some embodiments, the invention encompasses a method of providing afarmer with a means of controlling a lepidopteran insect pest, themethod comprising supplying or selling to the farmer plant material suchas a seed, the plant material comprising a polynucleotide, chimericgene, expression cassette or a recombinant vector capable of expressinga Cry protein of the invention, as described above.

Embodiments of this invention can be better understood by reference tothe following examples. The foregoing and following description ofembodiments of the invention and the various embodiments are notintended to limit the claims, but are rather illustrative thereof.Therefore, it will be understood that the claims are not limited to thespecific details of these examples. It will be appreciated by thoseskilled in the art that other embodiments of the invention may bepracticed without departing from the spirit and the scope of thedisclosure, the scope of which is defined by the appended claims.

EXAMPLES Example 1 Identification of Active Bt Strains

Bacillus thuringiensis isolates were cultured from spores present incurrent collections and maintained on T3+ penicillin agar plates. Eachisolate was grown aerobically in 24 well deep blocks for about 10 daysat 28° C. until sporulation, which was verified by staining withCoomasie blue/acetic acid and visualization with a microscope. Aftersporulation both the soluble and insoluble fractions were tested foractivity against lepidopteran species of interest. Fractions were testedin a surface contamination bioassay, where the fractions were overlaidonto a multispecies artificial diet. Each isolate was screened againstat least four lepidopteran species, including Helicoverpa zea (cornearworm), Agrotis ipsilon (black cutworm), Ostrinia nubilalis (Europeancorn borer), and Spodoptera frugiperda (fall armyworm) with a samplesize of 12 neonate larvae. The duration of each assay was about 7 daysat room temperature; the plates were scored for mortality as well aslarval growth inhibition. Observed mortality at an increase of 30% overthe negative control was considered active. Based on the initial insecttesting, strains C0588, C0633, C0680 and M0262 were selected for furtheranalysis.

Example 2 Isolation and Sequencing of Bt Genes

Fosmid Genomic Library Construction: For some Bt strains that wereidentified in Example 1, genes encoding the putatively active proteinswere isolated using a fosmid library method described in Park et al.(FEMS Microbiol. Lett. 284:28-34 (2008). The fosmid library wasconstructed using a CopyControl™ Fosmid Library Production Kit(Epicentre, Madison, Wis.) according to the manufacturer's protocol.Briefly, purified DNA from each Bt strain (approximately 0.5 μg) wastreated enzymatically to end repair the blunt ends, and was then ligatedinto the fosmid vector pCC1FOS (Epicentre). After in vitro packaginginto lambda phages and infection of Escherichia coli (E. coli)EP11300-T1®, the bacterial cells were plated on Luria-Bertani (LB) thatcontained 12.5 μg/ml chloramphenicol. The plates were incubated at about37° C. for 24 h before the selection of colonies. Transfected E. colicolonies were transferred to 96-well plates that contained 150 μl ofchloramphenicol-containing LB medium and were incubated at 37° C. for 24h.

Colony Hybridization Screen: A fosmid library was plated at a density of300 cfu per 100×15 mm L-agar plus 15 μg/ml chloramphenicol plate. Atotal of 3000 fosmids were plated. The filter hybridizations wereperformed using Immobilon-Ny+87 mm filter circles (EMD Millipore,Billerica, Mass.). Colony lifts were completed as follows: filters wereplaced on plates for about 5 min, then using forceps, filters werelifted from the agar surface and placed colony side up on Whatman filterpaper soaked with 0.5 M NaOH for 5 min. Colony filters were then placedon Whatman filter paper soaked in 2×SSC for 5 min. DNA was immobilizedto the membrane with a UV Stratalinker® set at 2000×1000 (Stratagene,Inc., La Jolla, Calif.). The filters are then air dried on Whatmanfilter paper. Filters were pre-hybridized and hybridized in 250 mMNaPO4, pH 7.0, 7% SDS, 1% BSA at 65° C. as described by the supplier.Hybridization filters were washed in 2×SSC, 0.5% SDS for 30 min at 65°C., followed by 0.2×SSC, 0.2% SDS for 30 min at 65° C. Filters wereexposed to X-ray film (Kodak® BIOMAX® XAR, Fisher Scientific,Pittsburgh, Pa.) overnight with intensifying screens at −80° C. Positivecolonies were patched to L agar with plus 15 μg/ml chloramphenicol.

Hybridization Probes: PCR primers were designed to amplify a 720 bpfragment of a cry9B-like gene from the genomic DNA of a Bt straindesignated C0633. The primer pair included a forward primer designatedOAR2613a having the sequence AAACATGAACCGAAATAATCAAAATG (SEQ ID NO:26)and a reverse primer designated OAR2615a having the sequenceATCCGTCCCTTGTGCGTGTAAA (SEQ ID NO:27). The PCR reaction was run underthe following cycle conditions: [94° C., 5 min], 12×[94° C., 30 sec, 57°C. to 51° C., dropping 0.5° C. per cycle, 30 sec, 72° C. 2.5 min], and35× [94° C., 30 sec, 52° C., 30 sec, 72° C., 2.5 min]. The reactioncontained 1× One Taq® buffer (New England Biolabs, Beverly, Mass.), 200um dNTP, 80 ng DNA, 2.5U One Taq® DNA polymerase, 50 ng each primer andsterile distilled water to 50 μl total reaction.

The resulting amplicon was separated on 1% agarose TAE gel containingethidium bromide. The amplicon was viewed under UV light and cut out ofthe gel. The DNA was isolated using a gel extraction kit as described bythe supplier (Qiagen, Valencia, Calif.). Probes were labeled withEasyTide ({acute over (α)}-32P) dCTP 3000 Ci/mmol (Perkin Elmer,Waltham, Mass.) using Rediprime II random prime labeling system (GEHealthcare, Pittsburgh, Pa.). Unincorporated nucleotides were removedusing Micro Bio-Spin 30 Chromatography columns (Biorad, Hercules,Calif.). Probes were heated at 95° C. for 5 min before addition tohybridization solution.

Bt Gene Sequencing: DNA preps for 2-4 independent clones are preppedfollowing the manufacturer's instructions (Qiagen). Sequencing reactionswith primers designed to both strands of the predicted nucleotidesequence of interest were carried out using the BigDye™ Terminator Kit(Applied Biosystems, Foster City, Calif.) according to manufacturer'sinstructions. Reaction products were electrophoresed on ABI373 or ABI377sequencing instruments. All sequencing data are analyzed using thePhred/Phrap/Consed software package (University of Washington) to anerror ratio equal to or less than 10⁻⁴ at the consensus sequence level.The sequence was assembled with the program Sequencher™ (Version 4.7,Gene Codes Corp., Ann Arbor, Mich.). Each gene was sequenced to 4×coverage.

Example 3 Bt Gene Cloning and Synthesis

Cry9-specific primer pairs were designed to facilitate theidentification and cloning of cry9-type genes. Primer pairs weredesigned to hybridize to a 5′ end of a cry9-type gene with the additionof a PmeI restriction site and to a 3′ end with the addition of an AsclIrestriction site. The primer pair used to amplify a 5′ end included aforward primer having the sequence

(SEQ ID NO: 28) GTTTAAACATGAATCGAAATAATCAAAATGand a reverse primer having the sequence

(SEQ ID NO: 29) GGCGCGCCCTACTCTTGTGTTTCAATAAA.The primer pair used to amplify a 3′ end included a forward primerhaving the sequence

(SEQ ID NO: 30) GTTTAAACATGAATCAAAATAAACACGGAand a reverse primer having the sequence

(SEQ ID NO: 31) GGCGCGCCTTACTGTTGGGTTTCCATGAACT.The inserted restriction sites are underlined in the respective primers.The PCR reactions were carried out using the following cycle conditions:[94° C., 5 min] and 30× [94° C., 30 sec, 45° C., 30 sec, 72° C., 3.5min]. The reaction contained 1× OneTaq buffer, 200 um dNTP, 80 ng DNA,2.5U OneTaq DNA polymerase (New England Biolabs), 50 ng each primer andsterile distilled water to 50 μl total reaction.

The resulting amplicon was cloned into the TOPO pCR 4.0 vector asdescribed by the supplier (Life Technologies). Isolated plasmid DNA wasdigested with PmeI and AscI as described by the supplier (New EnglandBiolabs).

The PmeI/AscI fragment was cloned into a shuttle vector designatedpCIB5634′ designed for expression in both E. coli and B. thuringiensis.The pCIB5634′ vector was digested with PmeI and AscI. The digestedvector and the gene fragment were purified by running on a 1% agaroseTris Acetate EDTA buffer based gel. The fragments were cutout from thegel and cleaned up using the QIAGEN gel extraction kit as described bythe supplier. The fragments were ligated together using a ligation kitfrom New England Biolabs as described by the supplier. The ligationreaction was transformed into TOP10 cells (Life Technologies) asdescribed by the supplier and plated on L-agar containing 100 mg/mlampicillin. Plasmid DNA was isolated from a single colony and theidentified clone was sequenced again to 2× coverage to confirm thecorrect sequence.

Some Bt genes that were selected for recombinant production but were notdirectly cloned out of genomic DNA were submitted to third party vendorsfor whole gene synthesis. These synthesized Bt genes were sub-clonedinto the above-described shuttle vectors for subsequent expression andtesting for further biological activity.

Example 4 Genome Assembly and Analysis

Some Bt genes of the invention were identified using a whole genomesequencing approach. Briefly, Bacillus DNA was sheared using a CovarisS2 ultrasonic device (Covaris, Inc., Woburn, Mass.) with the programDNA_400 bp set at duty cycle: 10%; intensity: 4; cycles/burst: 200. TheDNA was treated with the NEBNext® Ultra™ End Repair/dA-tailing module(New England Biolabs, Inc. Ipswich, Mass.). Biooscience indexes 1-57adapters (1-27 Brazil, 28-57 USA, UK and Switzerland) were ligated usingNEB Quick Ligation™ as described by the supplier (New England Biolabs,Inc. Ipswich, Mass.). Ligations were cleaned up using Agencourt AMPureXP beads as described by the supplier (Beckman Coulter, Inc.,Indianapolis, Ind.).

The library was size fractionated as follows: A 50 uL sample was mixedwith 45 ul 75% bead mix (25% AMPure beads plus 75% NaCl/PEG solutionTekNova cat #P4136). The mix was stirred and placed on magnetic rack.The resulting supernatant was transferred to a new well and 45 ul 50%bead mix (50% AMPure beads plus 50% NaCl/PEG solution TekNova cat#P4136) was added. This mix was stirred and placed on a magnetic rack.The resulting supernatant was removed and the beads were washed with 80%ethanol. 25 uL of elution buffer (EB) buffer was added and the mixplaced on a magnetic rack. The final resulting supernatant was removedand placed in 1.5 mL tube. This method yielded libraries in the 525 DNAbase pairs (bp) (insert plus adapter) size range.

The sized DNA library was amplified using KAPA Biosystem HiFi Hot Start(Kapa Biosystems, Inc., Wilmington, Mass.) using the following cycleconditions: [98° C., 45 s]; 12× [98° C., 15s, 60° C., 30 s, 72° C., 30s]; [72° C., 1 min]. Each reaction contained: 5 ul DNA library, 1 uLBioscience universal primer (25 uM), 18 uL sterile water, 1 uLBioscience indexed primer (25 uM), 25 ul 2× KAPA HiFi polymerase.

Libraries were run on the Agilent 2100 Bioanalyzer (AgilentTechnologies, Santa Clara, Calif.) using High Sensitivity chips todetermine the library size range and average insert size. All librarieswere processed for paired end (PE) sequencing (100 cycles per read;12-24 libraries per lane) on a HiSeq 2500 sequencing system usingstandard manufacturer's sequencing protocols (Illumina, Inc., San Diego,Calif.).

A Bacillus computational analysis tool was developed in order toidentify and characterize likely toxin genes for prioritization of leadsfor further laboratory testing.

The genome assembly and analysis as well as the genomic library analysisdescribed above led to the identification of five Cry9-like genes in theBacillus thuringiensis strains with toxicity to at least European cornborer (Ostrinia nubilalis). Identifying characteristics of the Cry9-likegenes and proteins are shown in Table 1.

TABLE 1 Cry9-like genes identified in Bacillus thuringiensis strains.Protein/Gene Molecular Nucleotide Amino Acid Strain Name Weight (kD) SEQID NO: SEQ ID NO: C0588 BT0009 132.2 1 19 C0633 BT0012 129.7 2 20 C0633BT0013 129.6 3 21 C0680 BT0023 130.8 4 22 M0262 BT0067 130.3 7 25

Example 5 Homology of BT0009, BT0012, BT0013, BT0023 and BT0067 to KnownBt Cry Proteins

A search of protein databases with the amino acid sequences of theproteins of the invention reveal that they are homologous to knowninsecticidal proteins. Comparison of the amino acid sequences of theproteins of the invention to the non-redundant (nr) database maintainedby the NCBI using the BLAST algorithm revealed the following proteins ashaving the strongest block of amino acid identity to the sequences ofthe invention (Table 2).

TABLE 2 Percent identity of Cry proteins of the invention with known Cryproteins. Percent Identity Cry9Aa1 Cry9Ba1 Cry9Bb1 Cry9Ca1 Cry9Da1Cry9Db1 Cry9Ea1 CryFa1 CryGa1 0009 60 70 66 66 82 88 67 64 36 0012 97 5753 56 56 56 56 52 62 0013 97 57 53 56 56 56 56 52 62 0023 59 70 65 70 7371 86 67 36 0067 59 69 66 75 76 74 76 69 36

Example 6 Bt Protein Expression in Recombinant Host Cells

Bacillus Expression. Genes of interest were expressed in anacrystalliferous Bacillus strain with no observable coleopteran orlepidopteran activity via the pCIB5634′ expression vector describedabove, which contains an appropriate Cry protein promoter anderythromycin resistance marker. Constructs were transformed into thehost strain via electroporation and subsequent selection on erythromycincontaining agar plates. These recombinant strains were grown tosporulation phase in T3 media at 28° C. for 4-5 days. Cell pellets wereharvested and washed iteratively before solubilization in high pHcarbonate buffer (50 mM) containing 2 mM DTT.

E. coli Expression. Genes of interest were expressed in various E. colistrains using the pET28a or pET29a vectors (EMD Millipore). Constructswere transformed by electroporation and subsequent selection onkanamycin-containing agar plates. These recombinant strains were grownand expression induced using IPTG induction at 28° C. Cells wereresuspended in high pH carbonate buffer (50 mM) containing 2 mM DTT andthen broken using a Microfluidics LV-1 homogenizer.

Expression Analysis. Resulting cell lysates (from either host) were thenclarified via centrifugation and samples were analyzed for purity viaSDS-PAGE and electropherogram (BioRad Experion). Total proteinconcentrations were determined via Bradford or Thermo 660 assay.Purified Cry proteins were then tested in bioassays.

Example 7 Activity of Cry Proteins in Bioassays

The proteins produced in Example 6 were tested against one or more ofthe following insect pest species using an art-recognized artificialdiet bioassay method: fall armyworm (FAW; Spodoptera frugiperda), cornearworm (CEW; Helicoverpa zea), European corn borer (ECB; Ostrinianubilalis), black cutworm (BCW; Agrotis Ipsilon), sugarcane borer (SCB;Diatraea saccharlis), velvet bean caterpillar (VBC; Anticarsiagemmatalis), soybean looper (SBL; Pseudoplusia includens), southwesterncorn borer (SWCB; Diatraea grandiosella), western bean cutworm (WBCW;Striacosta albicosta), tobacco budworm (TBW; Heliothis virescens), Asiancorn borer (ACB; Ostrinia furnacalis), cotton bollworm (CBW; Helicoverpaarmigera), striped stem borer (SSB; Chilo suppressalis), pink stem borer(PSB; Sesamia inferens) and rice leaf folder (RLF; Cnaphalocrocismedinails).

An equal amount of protein in solution was applied to the surface of anartifical insect diet (Bioserv, Inc., Frenchtown, N.J.) in 24 wellplates. After the diet surface dried, larvae of the insect species beingtested were added to each well. The plates were sealed and maintained atambient laboratory conditions with regard to temperature, lighting andrelative himidity. A positive-control group consisted of larvae exposedto a very active and broad-spectrum wild-type Bacillus strain. Negativecontrol groups consisted of larvae exposed to insect diet treated withonly the buffer solution and larvea on untreated insect diet; i.e. dietalone. Mortality was assessed after about 120 hours and scored relativeto the controls.

Results are shown in Table 3, where a “—” means no activity compared tocheck, a “+/−” means 0-10% activity compared to check (this categoryalso includes 0% mortality with strong larval growth inhibition), a “+”means 10-25% activity compared to check, a “++” means 25-75% activitycompared to check, and a “+++” 75-100% activity compared to check.

TABLE 3 Results of bioassay with Cry Proteins. BT Proteins Insect 00090012 0013 0023 0067 FAW − − − − +/− CEW − ++ + + − ECB +++ +++ +++ ++++++ BCW − − − − − SCB ++ ++ + VBC +++ +++ − SBL − +++ − SWCB ++ +++ +/−WBCW TBW +++ ++ ACB CBW SSB PSB RLF

Example 8 Fate of Cry Proteins in Simulated Gastric Fluid Assay

Certain Cry proteins have been expressed in plants and seed from suchplants are sold annually to farmers for use in controlling variousinsect pests. Such self-protected pesticidal products are subject toreview and registration by various regulatory agencies including, forexample, the US Environmental Protection Agency (EPA).

Dietary exposure is the major route by which humans can be exposed toCry proteins expressed in transgenic plants. Acute oral mammaliantoxicity and protein digestibility are the end points for EPA's humanhealth risk assessment. Further scientific evidence of the safety of Cryproteins is that they have been shown to be rapidly degraded in vitrousing simulated gastric fluids. Results of seven in vitro assaysconducted with representative Cry1, Cry2, and Cry3 proteins establishthat the proteins are rapidly degraded, typically within 30 seconds.These results support the broader conclusion that members of thesegroups of Cry proteins (that share significant amino acid sequenceidentity) are likely to be rapidly degraded following ingestion byhumans. Another area of consideration is whether Cry proteins may inducean allergenic reaction. The demonstrated rapid in vitro degradation ofCry proteins should minimize the potential for such an occurrence. Bycomparison, food allergens generally persisted in the in vitrogastrointestinal model, whereas common food proteins with no allergenichistory degraded rapidly in simulated gastric fluid (Metcalfe et al.1996).

Additional insights into the potential allergenicity of a protein can begained through an analysis of the protein's digestibility in simulatedgastric fluid (SGF). Almost all Cry proteins expressed in transgenicplants that have been tested to date are rapidly digested and thereforehave been determined to be non-allergenic. However, a Cry9C proteinfound in the transgenic corn product known as Starlink was found to bepartially stable to SGF. Although Starlink Cry9C is not toxic toanimals, the properties of partial digestibility and partial processingstability made it difficult for the EPA to absolutely preclude thepossibility that the Starlink Cry9C protein could act a food allergenultimately leading the company that developed Starlink to recallproducts from the US market.

Currently, no definitive tests for determining the allergenic potentialof novel proteins exist. Therefore, EPA uses a weight-of-evidenceapproach where the following factors are considered: source of thetrait; amino acid sequence comparison with known allergens; andbiochemical properties of the protein, including in vitro digestibilityin simulated gastric fluid (SGF) and glycosylation.

A simulated gastric fluid (SGF) assay measures the in vitrodigestibility of a test protein at tightly controlled conditionsrepresentative of the upper mammalian digestive tract. In brief,bacterially produced test Cry protein (at a concentration of 0.5-5mg/ml) was exposed to the enzyme pepsin (from porcine gastric mucosa,solubilized in 2 mg/ml NaCl, pH 1.2) at a ratio of 10 Units of pepsinactivity/μg test protein over a time period of one hour at 37° C.Samples are removed at 1,2,5,10,30, and 60 minutes and immediatelyquenched with the addition of pre-heated (95° C.—2 minutes) stop buffer(65% 0.5M Sodium Bicarbonate pH 11, 35% Tricine Loading Buffer) toimmediately render pepsin inactive, and returned to heat for anadditional 5 minutes. Once the assay was complete, time point samplesand controls (test protein alone, pepsin alone) were examined bySDS-PAGE on a 10-20% Tris-Tricine gel (with peptides visible down to 1kDa) to track the kinetics and level of digestion performed by pepsin.

Results of the SGF assays demonstrated that all of the Cry proteins ofthe invention were degraded very rapidly. These results provide evidencethat although the Cry proteins of the invention are related to the Cry 9protein family, they are quite different in their response to the SGFassay compared to certain published results, for example Cry9C inStarlink, suggesting significant structural differences at key pepsincleavage sites in the protein. These results further suggest that thepotential for the Cry proteins of the invention to be allergenic isminimal.

Example 9 Vectoring of Genes for Plant Expression

Prior to expression in plants, a synthetic polynucleotide comprising anucleotide sequence encoding each of the Bt Cry proteins, BT-0009,BT-0012, BT-0013, BT-0023 and BT-0067 (SEQ ID NOs:6-10, respectively),and a synthetic polynucleotide comprising a nucleotide sequence encodingeach of the mutant Bt Cry proteins, mBT-0009, mBT-0012, mBT-0013,mBT-0023 and mBT-0067 (SEQ ID NOs:21-25, respectively) was synthesizedon an automated gene synthesis platform (Genscript, Inc., Piscataway,N.J.). For this example, a first expression cassette was made comprisinga maize ubiquitin promoter (Ubil) operably linked to the Cry proteincoding sequence which was operably linked to a Nos terminator and asecond expression cassette was made comprising a Ubi1 promoter operablylinked to a phosphomannose isomerase (PMI) coding sequence which wasoperably linked to a Nos terminator. Expression of PMI allows forpositive selection of transgenic plants on mannose. Both expressioncassettes were cloned into a suitable vector for Agrobacterium-mediatedmaize transformation.

Example 11 Expression of Cry Proteins in Plants

Transformation of immature maize embryos is performed essentially asdescribed in Negrotto et al., 2000, Plant Cell Reports 19: 798 803.Briefly, Agrobacterium strain LBA4404 (pSB1) comprising a vectordescribed in Example 12 is grown on YEP (yeast extract (5 g/L), peptone(10 g/L), NaCl (5 g/L), 15 g/l agar, pH 6.8) solid medium for 2-4 daysat 28° C. Approximately 0.8×10⁹ Agrobacterium cells are suspended inLS-inf media supplemented with 100 μM As. Bacteria are pre-induced inthis medium for approximately 30-60 minutes.

Immature embryos from an inbred maize line are excised from 8-12 day oldears into liquid LS-inf+100 μM As. Embryos are rinsed once with freshinfection medium. Agrobacterium solution is then added and embryos arevortexed for 30 seconds and allowed to settle with the bacteria for 5minutes. The embryos are then transferred scutellum side up to LSAsmedium and cultured in the dark for two to three days. Subsequently,between approximately 20 and 25 embryos per petri plate are transferredto LSDc medium supplemented with cefotaxime (250 mg/l) and silvernitrate (1.6 mg/l) and cultured in the dark at approximately 28° C. for10 days.

Immature embryos, producing embryogenic callus are transferred toLSD1M0.5S medium. The cultures are selected on this medium forapproximately 6 weeks with a subculture step at about 3 weeks. Survivingcalli are transferred to Regl medium supplemented with mannose.Following culturing in the light (16 hour light/8 hour dark regiment),green tissues are then transferred to Reg2 medium without growthregulators and incubated for about 1-2 weeks. Plantlets are transferredto Magenta GA-7 boxes (Magenta Corp, Chicago Ill.) containing Reg3medium and grown in the light. After about 2-3 weeks, plants are testedfor the presence of the PMI genes and the Bt cry gene by PCR. Positiveplants from the PCR assay are transferred to a greenhouse for furtherevaluation.

Transgenic plants are evaluated for copy number (determined by Taqmananalysis), protein expression level (determined by ELISA), and efficacyagainst insect species of interest in leaf excision bioassays.Specifically, leaf tissue is excised from single copy events (V3-V4stage) and infested with neonate larvae, then incubated at roomtemperature for 5 days. Sample size for leaf disk bioassay variesdepending on the insect species tested (European corn borer (ECB), n=10;corn earworm (CEW), n=3, black cutworm (BCW), n=5). Readings to assesstissue damage and mortality are taken at approximately day 3 and day 5;samples are rated for damage relative to the negative control using thefollowing scale: “+”: <5% tissue damage, all larvae dead; “+/−”: 5-20%tissue damage, all larvae dead; or “−”: >20% tissue damage, some larvaealive and/or progressing to 2^(nd) instar.

Results of the transgenic plant tissue bioassay confirm that the Cryproteins of the invention when expressed in transgenic plants are toxicto target insects. For example, mBT-0012 expressed in maize stablytransformed with a chimeric gene of the invention is active against atleast European corn borer (Ostrinia nubilalis).

What is claimed is:
 1. A chimeric gene comprising a heterologouspromoter operably linked to a nucleic acid molecule comprising anucleotide sequence that encodes a protein toxic to at least Europeancorn borer (Ostrinia nubilalis), wherein the nucleotide sequence (a)comprises SEQ ID NO:2; or (b) encodes a protein comprising an amino acidsequence that has at least 99% sequence identity across its full lengthwith SEQ ID NO:22; or (c) is a synthetic sequence of (a) or (b) that hascodons optimized for expression in a transgenic organism.
 2. Thechimeric gene of claim 1, wherein the nucleotide sequence comprises SEQID NO:2.
 3. The chimeric gene of claim 1, wherein the nucleotidesequence encodes a protein comprising SEQ ID NO:17 or SEQ ID NO:22.
 4. Asynthetic nucleic acid molecule comprising a nucleotide sequence thatencodes a protein that is toxic to at least European corn borer(Ostrinia nubilalis), wherein the nucleotide sequence has codonsoptimized for expression in a transgenic organism compared to SEQ IDNO:2 and encodes an amino acid sequence that has at least 99% sequenceidentity across its full length with SEQ ID NO:22.
 5. The syntheticnucleic acid molecule of claim 4, wherein the nucleotide sequencecomprises SEQ ID NO:7 or SEQ ID NO:12.
 6. The synthetic nucleic acidmolecule of claim 4, wherein the nucleotide sequence encodes SEQ IDNO:17 or SEQ ID NO:22.
 7. A mutant insecticidal protein that is toxic toat least European corn borer (Ostrinia nubilalis), wherein the proteincomprises an amino acid sequence that has at least 95% sequence identityacross its full length to SEQ ID NO:22 and has one or more amino acidsubstitutions compared to SEQ ID NO:17.
 8. The protein of claim 7,wherein the amino acid sequence comprises SEQ ID NO:22.
 9. Aninsecticidal composition comprising the protein of claim 7 and anagriculturally acceptable carrier.
 10. A recombinant vector comprisingthe chimeric gene of claim
 1. 11. A transgenic plant comprising thechimeric gene of claim
 12. Transgenic seed of the transgenic plant ofclaim 9, wherein said seed comprises the chimeric gene.
 13. A method ofproducing an insect-resistant transgenic plant, said method comprising:introducing into a plant the chimeric gene of claim 1, wherein theinsecticidal protein is expressed in the plant, thereby conferring tothe plant resistance to at least European corn borer (Ostrinianubilalis), and producing an insect-resistant transgenic plant.
 14. Amethod of controlling at least European corn borer (Ostrinia nubilalis)insects, said method comprising delivering to the insects an effectiveamount of a protein encoded by the chimeric gene of claim 1.